diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a88c8ee5b..87bd78c88f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [4.3.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.2.0...v4.3.0) (2024-08-28) + + +### Features + +* add support for multiple input file subcommands in seqkit wrapper (subcommands "common" and "concat") ([#3142](https://www.github.com/snakemake/snakemake-wrappers/issues/3142)) ([3b5391f](https://www.github.com/snakemake/snakemake-wrappers/commit/3b5391f619b38334829c06b8bd0526a16e19c732)) +* Deeptools multibigwig summary ([#3135](https://www.github.com/snakemake/snakemake-wrappers/issues/3135)) ([df7e2bf](https://www.github.com/snakemake/snakemake-wrappers/commit/df7e2bffdd61690e56380bb1b49ca663e58a477c)) +* Deeptools plot correlation ([#3137](https://www.github.com/snakemake/snakemake-wrappers/issues/3137)) ([a965bd6](https://www.github.com/snakemake/snakemake-wrappers/commit/a965bd62f13bb62722daf08201a00b1f26bef38d)) +* Deeptools plot pca ([#3138](https://www.github.com/snakemake/snakemake-wrappers/issues/3138)) ([0d9862b](https://www.github.com/snakemake/snakemake-wrappers/commit/0d9862b0f91e74bb90993eb7ecb938dec80d779b)) +* Rseqc bamstat ([#3139](https://www.github.com/snakemake/snakemake-wrappers/issues/3139)) ([b4267e6](https://www.github.com/snakemake/snakemake-wrappers/commit/b4267e6a0244071a96efc8a91fd6ba982a738cb5)) +* Rseqc inner distance ([#3140](https://www.github.com/snakemake/snakemake-wrappers/issues/3140)) ([8ca10f3](https://www.github.com/snakemake/snakemake-wrappers/commit/8ca10f3949ca6fb1ed9f9d046c89ca10a7c32c8c)) + ## [4.2.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.1...v4.2.0) (2024-08-23) diff --git a/bio/adapterremoval/environment.linux-64.pin.txt b/bio/adapterremoval/environment.linux-64.pin.txt index 7dfdff7ccf..0bfde58210 100644 --- a/bio/adapterremoval/environment.linux-64.pin.txt +++ b/bio/adapterremoval/environment.linux-64.pin.txt @@ -3,13 +3,15 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54 -https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-4_hd590300_perl5.conda#3e785bff761095eb7f8676f4694bd1b1 -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209 -https://conda.anaconda.org/bioconda/linux-64/adapterremoval-2.3.3-pl5321h6dccd9a_2.tar.bz2#406badf77e01e3a1d2c86416152811f4 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/bioconda/linux-64/adapterremoval-2.3.4-pl5321h6dccd9a_0.tar.bz2#46295c24fb766dd0a862af6b0e4f82b5 diff --git a/bio/adapterremoval/environment.yaml b/bio/adapterremoval/environment.yaml index 90c6cc7618..339c682594 100644 --- a/bio/adapterremoval/environment.yaml +++ b/bio/adapterremoval/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - adapterremoval =2.3.3 + - adapterremoval =2.3.4 diff --git a/bio/bwameth/index/meta.yaml b/bio/bwameth/index/meta.yaml index 815a7cca90..e741c5b0dc 100644 --- a/bio/bwameth/index/meta.yaml +++ b/bio/bwameth/index/meta.yaml @@ -1,5 +1,5 @@ name: bwa-meth index -url: https://github.com/brentp/bwa-meth?tab=readme-ov-file#index +url: https://github.com/brentp/bwa-meth description: > Index a reference sequence for future BS-Seq mapping. authors: diff --git a/bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt b/bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt new file mode 100644 index 0000000000..862c8f70ed --- /dev/null +++ b/bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt @@ -0,0 +1,112 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb +https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 +https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f +https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hd590300_1.conda#aec6c91c7371c26392a06708a73c70e5 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 +https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace +https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-hd590300_1.conda#323e90742f0f48fc22bea908735f55e6 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0 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https://deeptools.readthedocs.io/en/develop/content/tools/multiBigwigSummary.html +description: > + Compute the average scores for each of the files in every genomic region. +authors: + - Thibault Dayris +input: + - bw: Path to a bigwig file, or a list of bigwig files. + - blacklist: Optional path to a BED file covering regions to exclude. + - bed: Path to a bed file to limit the analysis of regions. This triggers the subcommand `BED-file`. Leave empty to run the `bins` subcommand. +output: + - npz: Path to the compressed matrix file. + - counts: Path to average scores per region for each bigwig. +params: + - extra: Optional arguments for `multiBigwigSummary` besides IO and processor. +notes: | + Subcomand is automatically inferred from the presence of `input.bed` (optional) key. diff --git a/bio/deeptools/multibigwigsummary/test/Snakefile b/bio/deeptools/multibigwigsummary/test/Snakefile new file mode 100644 index 0000000000..49a9ffbee5 --- /dev/null +++ b/bio/deeptools/multibigwigsummary/test/Snakefile @@ -0,0 +1,33 @@ +rule test_deeptools_multibwsummary_bins: + input: + bw=["a.bw", "b.bw"], + blacklist="blacklist.bed", # Optional + output: + npz="bins.npz", + counts="bins.counts", + threads: 1 + params: + extra="", + log: + "bins.logs" + wrapper: + "master/bio/deeptools/multibigwigsummary" + +rule test_deeptools_multibwsummary_bed: + input: + bw=["a.bw", "b.bw"], + bed="intervals.bed", + # blacklist="", # Optional + output: + npz="bed.npz", + counts="bed.counts", + threads: 1 + params: + extra="", + log: + "bins.logs" + wrapper: + "master/bio/deeptools/multibigwigsummary" + + + diff --git a/bio/deeptools/multibigwigsummary/test/a.bw b/bio/deeptools/multibigwigsummary/test/a.bw new file mode 100644 index 0000000000..dc1aa69854 Binary files /dev/null and b/bio/deeptools/multibigwigsummary/test/a.bw differ diff --git a/bio/deeptools/multibigwigsummary/test/b.bw b/bio/deeptools/multibigwigsummary/test/b.bw new file mode 100644 index 0000000000..672f679ae1 Binary files /dev/null and b/bio/deeptools/multibigwigsummary/test/b.bw differ diff --git a/bio/deeptools/multibigwigsummary/test/blacklist.bed b/bio/deeptools/multibigwigsummary/test/blacklist.bed new file mode 100644 index 0000000000..8bfb98986b --- /dev/null +++ b/bio/deeptools/multibigwigsummary/test/blacklist.bed @@ -0,0 +1,2 @@ +1 1 20 +2 15 30 diff --git a/bio/deeptools/multibigwigsummary/test/intervals.bed b/bio/deeptools/multibigwigsummary/test/intervals.bed new file mode 100644 index 0000000000..a24aa37011 --- /dev/null +++ b/bio/deeptools/multibigwigsummary/test/intervals.bed @@ -0,0 +1,3 @@ +1 10 40 +1 100 150 +2 1 20 diff --git a/bio/deeptools/multibigwigsummary/wrapper.py b/bio/deeptools/multibigwigsummary/wrapper.py new file mode 100644 index 0000000000..2f75ea0d60 --- /dev/null +++ b/bio/deeptools/multibigwigsummary/wrapper.py @@ -0,0 +1,36 @@ +# coding: utf-8 + +__author__ = "Thibault Dayris" +__copyright__ = "Copyright 2024, Thibault Dayris" +__email__ = "thibault.dayris@gustaveroussy.fr" +__license__ = "MIT" + + +from snakemake.shell import shell + +# Optional parameters +log = snakemake.log_fmt_shell(stdout=True, stderr=True) +extra = snakemake.params.get("extra", "") + +blacklist = snakemake.input.get("blacklist") +if blacklist: + extra += f" --blackListFileName {blacklist} " + +out_raw_counts = snakemake.output.get("counts") +if out_raw_counts: + extra += f" --outRawCounts {out_raw_counts} " + +bed = snakemake.input.get("bed") +subcommand = "bins" +if bed: + subcommand = "BED-file" + extra += f" --BED {bed} " + + +shell( + "multiBigwigSummary {subcommand} " + "--bwfiles {snakemake.input.bw} " + "--outFileName {snakemake.output.npz} " + "--numberOfProcessors {snakemake.threads} " + "{extra} {log}" +) diff --git a/bio/deeptools/plotcorrelation/environment.linux-64.pin.txt b/bio/deeptools/plotcorrelation/environment.linux-64.pin.txt new file mode 100644 index 0000000000..862c8f70ed --- /dev/null +++ b/bio/deeptools/plotcorrelation/environment.linux-64.pin.txt @@ -0,0 +1,112 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef 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the output of multiBamSummary or multiBigwigSummary. +authors: + - Thibault Dayris +input: + - Path to compressed matrix file +output: + - plot: Path to scatterplot/heatmap. The available formats are `.png`, `.eps`, `.pdf` and `.svg` + - matrix: Optional path to pairwise correlation values (TSV) +params: + - extra: Optional parameters except IO and `--plotFileFormat`. + - correlation: Either `spearman`, or `pearson`. No default is set in DeepTools. This wrapper considers `spearman` as default value. + - plot: Either `heatmap`, or `scatterplot`. No default is set in DeepTools. This wrapper considers `heatmap` as default value. +notes: | + Plot file format is automatically inferred from plot file extension. diff --git a/bio/deeptools/plotcorrelation/test/Snakefile b/bio/deeptools/plotcorrelation/test/Snakefile new file mode 100644 index 0000000000..b192f2710c --- /dev/null +++ b/bio/deeptools/plotcorrelation/test/Snakefile @@ -0,0 +1,15 @@ +rule test_deeptools_plot_correlation: + input: + "bins.npz", + output: + plot="bins.svg", + counts="counts.tsv", # Optional output file + threads: 1 + params: + extra="--skipZeros", # Any optional parameters besides IO and --plotFileFormat + correlation="spearman", # either spearman or pearson + plot="heatmap", # either heatmap or scatterplot + log: + "corr.log", + wrapper: + "master/bio/deeptools/plotcorrelation" diff --git a/bio/deeptools/plotcorrelation/test/bins.npz b/bio/deeptools/plotcorrelation/test/bins.npz new file mode 100644 index 0000000000..1453053875 Binary files /dev/null and b/bio/deeptools/plotcorrelation/test/bins.npz differ diff --git a/bio/deeptools/plotcorrelation/wrapper.py b/bio/deeptools/plotcorrelation/wrapper.py new file mode 100644 index 0000000000..11434c2921 --- /dev/null +++ b/bio/deeptools/plotcorrelation/wrapper.py @@ -0,0 +1,35 @@ +# coding: utf-8 + +__author__ = "Thibault Dayris" +__copyright__ = "Copyright 2024, Thibault Dayris" +__email__ = "thibault.dayris@gustaveroussy.fr" +__license__ = "MIT" + + +from snakemake.shell import shell + +# Optional parameters +log = snakemake.log_fmt_shell(stdout=True, stderr=True) +extra = snakemake.params.get("extra", "") + +# Get required arguments +cor_method = snakemake.params.get("correlation", "spearman") +what_to_plot = snakemake.params.get("plot", "heatmap") + +# Get plot file format +fmt = str(snakemake.output["plot"]).split(".")[-1].lower() + +# Get optional output matrix +corr_matrix = snakemake.output.get("counts") +if corr_matrix: + extra += f" --outFileCorMatrix {corr_matrix} " + +shell( + "plotCorrelation " + "--corData {snakemake.input[0]} " + "--corMethod {cor_method} " + "--whatToPlot {what_to_plot} " + "--plotFile {snakemake.output.plot} " + "--plotFileFormat {fmt} " + "{extra} {log}" +) diff --git a/bio/deeptools/plotpca/environment.linux-64.pin.txt b/bio/deeptools/plotpca/environment.linux-64.pin.txt new file mode 100644 index 0000000000..862c8f70ed --- /dev/null +++ b/bio/deeptools/plotpca/environment.linux-64.pin.txt @@ -0,0 +1,112 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 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+https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.8.3-py310h62c0568_0.conda#4a7296c0273eb01dfbed728dd6a6725a +https://conda.anaconda.org/bioconda/noarch/deeptools-3.5.5-pyhdfd78af_0.tar.bz2#87a4bd9512e17fb7633a1386dbea5125 +https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.6.0-pyhd8ed1ab_0.conda#191b8a622191a403700d16a2008e4e29 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.8-pyhd8ed1ab_0.conda#611a35a27914fac3aa37611a6fe40bb5 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.6-pyhd8ed1ab_0.conda#d7e4954df0d3aea2eacc7835ad12671d +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8ed1ab_0.conda#7e1e7437273682ada2ed5e9e9714b140 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1 +https://conda.anaconda.org/conda-forge/noarch/sphinx-7.2.6-pyhd8ed1ab_0.conda#bbfd1120d1824d2d073bc65935f0e4c0 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e diff --git a/bio/deeptools/plotpca/environment.yaml b/bio/deeptools/plotpca/environment.yaml new file mode 100644 index 0000000000..65c1c44e66 --- /dev/null +++ b/bio/deeptools/plotpca/environment.yaml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - deeptools =3.5.5 diff --git a/bio/deeptools/plotpca/meta.yaml b/bio/deeptools/plotpca/meta.yaml new file mode 100644 index 0000000000..37e2dc5b03 --- /dev/null +++ b/bio/deeptools/plotpca/meta.yaml @@ -0,0 +1,15 @@ +name: Deeptools Plot Correlation +url: https://deeptools.readthedocs.io/en/develop/content/tools/plotPCA.html +description: > + Generate a principal component analysis (PCA) plot from multiBamSummary or multiBigwigSummary output. +authors: + - Thibault Dayris +input: + - Path to compressed matrix file +output: + - plot: Path to PCA plot. The available options are `.png`, `.eps`, `.pdf` and `.svg`. + - matrix: Optional path to the data underlying the plot. +params: + - extra: Optional parameters besides IO and `--plotFileFormat` +notes: > + Plot file format is automatically inferred from `output.plot` extension. diff --git a/bio/deeptools/plotpca/test/Snakefile b/bio/deeptools/plotpca/test/Snakefile new file mode 100644 index 0000000000..7578c624fb --- /dev/null +++ b/bio/deeptools/plotpca/test/Snakefile @@ -0,0 +1,13 @@ +rule test_deeptools_plot_pca: + input: + "bins.npz", + output: + plot="pca.svg", + matrix="pca.tab", # Optional + threads: 1 + params: + extra="--ntop 5", + log: + "pca.log", + wrapper: + "master/bio/deeptools/plotpca" diff --git a/bio/deeptools/plotpca/test/bins.npz b/bio/deeptools/plotpca/test/bins.npz new file mode 100644 index 0000000000..1453053875 Binary files /dev/null and b/bio/deeptools/plotpca/test/bins.npz differ diff --git a/bio/deeptools/plotpca/wrapper.py b/bio/deeptools/plotpca/wrapper.py new file mode 100644 index 0000000000..4956759b83 --- /dev/null +++ b/bio/deeptools/plotpca/wrapper.py @@ -0,0 +1,30 @@ +# coding: utf-8 + +__author__ = "Thibault Dayris" +__copyright__ = "Copyright 2024, Thibault Dayris" +__email__ = "thibault.dayris@gustaveroussy.fr" +__license__ = "MIT" + + +from snakemake.shell import shell + +# Optional parameters +log = snakemake.log_fmt_shell(stdout=True, stderr=True) +extra = snakemake.params.get("extra", "") + + +# Get plot file format +fmt = str(snakemake.output["plot"]).split(".")[-1].lower() + +# Get optional output matrix +pca_tab = snakemake.output.get("matrix") +if pca_tab: + extra += f" --outFileNameData {pca_tab} " + +shell( + "plotPCA " + "--corData {snakemake.input[0]} " + "--plotFile {snakemake.output.plot} " + "--plotFileFormat {fmt} " + "{extra} {log}" +) diff --git a/bio/emu/abundance/environment.linux-64.pin.txt b/bio/emu/abundance/environment.linux-64.pin.txt index a863eb447d..592d0b8b4d 100644 --- a/bio/emu/abundance/environment.linux-64.pin.txt +++ b/bio/emu/abundance/environment.linux-64.pin.txt @@ -3,60 +3,64 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_1.conda#10a0cef64b784d6ab6da50ebca4e984d +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.1-heb4867d_0.conda#0d3c60291342c0c025db231353376dfb https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.1.0-h69a702a_1.conda#591e631bc1ae62c64f2ab4f66178c097 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_1.conda#16cec94c5992d7f42ae3f9fa8b25df8d https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209 -https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589 -https://conda.anaconda.org/bioconda/linux-64/bioawk-1.0-he4a0461_10.tar.bz2#3f4ea155f59ae781753ea76571e8564a +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67 +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 +https://conda.anaconda.org/bioconda/linux-64/bioawk-1.0-he4a0461_12.tar.bz2#e7d93b174316328e1f98a7a0771ddc1b https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2 -https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844 -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155 -https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2 -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5 -https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d +https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda#b8afb3e3cb3423cc445cf611ab95fdb0 +https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_3.tar.bz2#0e2b1e20347eddfa294608536ded59cf https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.1-pyhd8ed1ab_0.conda#98206ea9954216ee7540f0c773f2104d https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad -https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/noarch/zipp-3.17.0-pyhd8ed1ab_0.conda#2e4d6bc0b14e10f895fc6791a7d9b26a -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.1.0-pyha770c72_0.conda#0896606848b2dc5cebdf111b6543aa04 -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838 -https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py310hff52083_3.conda#62d26790749f62b9329425c901d93c3a -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 -https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.0-py310h41dec4a_1.tar.bz2#19fdb9301a6debbb7fe9836670e3feb7 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda#74a4befb4b38897e19a107693e49da20 +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.4.0-pyha770c72_0.conda#6e3dbc422d3749ad72659243d6ac8b2b +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 +https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py312h7900ff3_3.conda#3d6a6028b8378ac14fc145ce4c5f88fa +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyh8b19718_1.conda#6c78fbb8ddfd64bcb55b5cbafd2d2c43 +https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.1-py312hcfdcdd7_2.tar.bz2#33baeca8a223d34355fd37bc9e14a128 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c https://conda.anaconda.org/conda-forge/noarch/flatten-dict-0.4.2-pyhd8ed1ab_1.tar.bz2#ccfb30b92adfeb283d4dcae3d0b6441b -https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be -https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py310h2372a71_0.conda#0128595946cebfaaf212cc45d4b9cd3c -https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py310hcc13569_0.conda#96910063174ce34fc15609081efc3e5d -https://conda.anaconda.org/bioconda/noarch/emu-3.4.5-hdfd78af_0.tar.bz2#34b067c6f82c3796a40e1b0ecaf094d3 +https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.0-py312h1103770_0.conda#9709027e8a51a3476db65a3c0cf806c2 +https://conda.anaconda.org/conda-forge/linux-64/biopython-1.84-py312h9a8786e_0.conda#6683d74a08fc106ef44d6ac403dc7aee +https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py312h1d6d2e6_1.conda#ae00b61f3000d2284d1f2584d4dfafa8 +https://conda.anaconda.org/bioconda/noarch/emu-3.4.6-hdfd78af_0.tar.bz2#6dd947250aaddea7918056f230ba8a4e diff --git a/bio/emu/abundance/environment.yaml b/bio/emu/abundance/environment.yaml index 81e14207d0..14dc71b455 100644 --- a/bio/emu/abundance/environment.yaml +++ b/bio/emu/abundance/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - emu =3.4.5 + - emu =3.4.6 diff --git a/bio/emu/collapse-taxonomy/environment.linux-64.pin.txt b/bio/emu/collapse-taxonomy/environment.linux-64.pin.txt index a863eb447d..592d0b8b4d 100644 --- a/bio/emu/collapse-taxonomy/environment.linux-64.pin.txt +++ b/bio/emu/collapse-taxonomy/environment.linux-64.pin.txt @@ -3,60 +3,64 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_1.conda#10a0cef64b784d6ab6da50ebca4e984d +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.1-heb4867d_0.conda#0d3c60291342c0c025db231353376dfb https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.1.0-h69a702a_1.conda#591e631bc1ae62c64f2ab4f66178c097 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_1.conda#16cec94c5992d7f42ae3f9fa8b25df8d https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b 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-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d +https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda#b8afb3e3cb3423cc445cf611ab95fdb0 +https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_3.tar.bz2#0e2b1e20347eddfa294608536ded59cf https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.1-pyhd8ed1ab_0.conda#98206ea9954216ee7540f0c773f2104d https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad -https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/noarch/zipp-3.17.0-pyhd8ed1ab_0.conda#2e4d6bc0b14e10f895fc6791a7d9b26a -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.1.0-pyha770c72_0.conda#0896606848b2dc5cebdf111b6543aa04 -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838 -https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py310hff52083_3.conda#62d26790749f62b9329425c901d93c3a -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 -https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.0-py310h41dec4a_1.tar.bz2#19fdb9301a6debbb7fe9836670e3feb7 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda#74a4befb4b38897e19a107693e49da20 +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.4.0-pyha770c72_0.conda#6e3dbc422d3749ad72659243d6ac8b2b +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 +https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py312h7900ff3_3.conda#3d6a6028b8378ac14fc145ce4c5f88fa +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyh8b19718_1.conda#6c78fbb8ddfd64bcb55b5cbafd2d2c43 +https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.1-py312hcfdcdd7_2.tar.bz2#33baeca8a223d34355fd37bc9e14a128 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c https://conda.anaconda.org/conda-forge/noarch/flatten-dict-0.4.2-pyhd8ed1ab_1.tar.bz2#ccfb30b92adfeb283d4dcae3d0b6441b -https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be -https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py310h2372a71_0.conda#0128595946cebfaaf212cc45d4b9cd3c -https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py310hcc13569_0.conda#96910063174ce34fc15609081efc3e5d -https://conda.anaconda.org/bioconda/noarch/emu-3.4.5-hdfd78af_0.tar.bz2#34b067c6f82c3796a40e1b0ecaf094d3 +https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.0-py312h1103770_0.conda#9709027e8a51a3476db65a3c0cf806c2 +https://conda.anaconda.org/conda-forge/linux-64/biopython-1.84-py312h9a8786e_0.conda#6683d74a08fc106ef44d6ac403dc7aee +https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py312h1d6d2e6_1.conda#ae00b61f3000d2284d1f2584d4dfafa8 +https://conda.anaconda.org/bioconda/noarch/emu-3.4.6-hdfd78af_0.tar.bz2#6dd947250aaddea7918056f230ba8a4e diff --git a/bio/emu/collapse-taxonomy/environment.yaml b/bio/emu/collapse-taxonomy/environment.yaml index 81e14207d0..14dc71b455 100644 --- a/bio/emu/collapse-taxonomy/environment.yaml +++ b/bio/emu/collapse-taxonomy/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - emu =3.4.5 + - emu =3.4.6 diff --git a/bio/emu/combine-outputs/environment.linux-64.pin.txt b/bio/emu/combine-outputs/environment.linux-64.pin.txt index a863eb447d..592d0b8b4d 100644 --- a/bio/emu/combine-outputs/environment.linux-64.pin.txt +++ b/bio/emu/combine-outputs/environment.linux-64.pin.txt @@ -3,60 +3,64 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_1.conda#10a0cef64b784d6ab6da50ebca4e984d +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.1-heb4867d_0.conda#0d3c60291342c0c025db231353376dfb https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.1.0-h69a702a_1.conda#591e631bc1ae62c64f2ab4f66178c097 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a 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b/bio/emu/combine-outputs/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - emu =3.4.5 + - emu =3.4.6 diff --git a/bio/last/lastal/environment.linux-64.pin.txt b/bio/last/lastal/environment.linux-64.pin.txt index e2532d4d89..d2bf8e21c7 100644 --- a/bio/last/lastal/environment.linux-64.pin.txt +++ b/bio/last/lastal/environment.linux-64.pin.txt @@ -6,23 +6,25 @@ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.ta https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 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https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908 @@ -30,7 +32,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 -https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hd590300_0.conda#151cba22b85a989c2d6ef9633ffee1e4 +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hb9d3cd8_1.conda#3601598f0db0470af28985e3e7ad0158 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc @@ -44,5 +46,5 @@ https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda# https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89 https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h287a98d_0.conda#59ea71eed98aee0bebbbdd3b118167c7 -https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 -https://conda.anaconda.org/bioconda/linux-64/last-1571-h43eeafb_0.tar.bz2#37196ba9aed615c5aa2a298e9d8adbd8 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyh8b19718_1.conda#6c78fbb8ddfd64bcb55b5cbafd2d2c43 +https://conda.anaconda.org/bioconda/linux-64/last-1574-h43eeafb_0.tar.bz2#389e4133b5b8f818cfd25a017a4d6e5b diff --git a/bio/last/lastal/environment.yaml b/bio/last/lastal/environment.yaml index 81144a4d92..363b44bcf6 100644 --- a/bio/last/lastal/environment.yaml +++ b/bio/last/lastal/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - last =1571 + - last =1574 diff --git a/bio/last/lastdb/environment.linux-64.pin.txt b/bio/last/lastdb/environment.linux-64.pin.txt index e2532d4d89..d2bf8e21c7 100644 --- a/bio/last/lastdb/environment.linux-64.pin.txt +++ b/bio/last/lastdb/environment.linux-64.pin.txt @@ -6,23 +6,25 @@ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.ta https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908 @@ -30,7 +32,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 -https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hd590300_0.conda#151cba22b85a989c2d6ef9633ffee1e4 +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hb9d3cd8_1.conda#3601598f0db0470af28985e3e7ad0158 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc @@ -44,5 +46,5 @@ https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda# https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89 https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h287a98d_0.conda#59ea71eed98aee0bebbbdd3b118167c7 -https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 -https://conda.anaconda.org/bioconda/linux-64/last-1571-h43eeafb_0.tar.bz2#37196ba9aed615c5aa2a298e9d8adbd8 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyh8b19718_1.conda#6c78fbb8ddfd64bcb55b5cbafd2d2c43 +https://conda.anaconda.org/bioconda/linux-64/last-1574-h43eeafb_0.tar.bz2#389e4133b5b8f818cfd25a017a4d6e5b diff --git a/bio/last/lastdb/environment.yaml b/bio/last/lastdb/environment.yaml index 81144a4d92..363b44bcf6 100644 --- a/bio/last/lastdb/environment.yaml +++ b/bio/last/lastdb/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - last =1571 + - last =1574 diff --git a/bio/open-cravat/module/environment.linux-64.pin.txt b/bio/open-cravat/module/environment.linux-64.pin.txt index a0984dd608..661db40d47 100644 --- a/bio/open-cravat/module/environment.linux-64.pin.txt +++ b/bio/open-cravat/module/environment.linux-64.pin.txt @@ -3,73 +3,84 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_1.conda#10a0cef64b784d6ab6da50ebca4e984d +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h3d2ce59_11.conda#c485da4fdb454539f852a90ae06e9bb7 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.1.0-h69a702a_1.conda#591e631bc1ae62c64f2ab4f66178c097 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_11.conda#eaa8ea74083fb4a78ae19e431e556003 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_11.conda#4c3e460d6acf8e43e4ce8bf405187eb7 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_1.conda#16cec94c5992d7f42ae3f9fa8b25df8d https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155 -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 -https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda#5e4c0743c70186509d1412e03c2d8dfa +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 +https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.4.0-pyhd8ed1ab_0.conda#0482cd2217e27b3ce47676d570ac3d45 +https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda#6732fa52eb8e66e5afeb32db8701a791 https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h30efb56_1.conda#45801a89533d3336a365284d93298e36 -https://conda.anaconda.org/conda-forge/noarch/certifi-2024.6.2-pyhd8ed1ab_0.conda#8821ec1c8fcdc9e1d291d7b9f6e9968a -https://conda.anaconda.org/conda-forge/linux-64/chardet-5.2.0-py312h7900ff3_1.conda#af3980cc4690716a5510c8a08cb06238 +https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda#24e7fd6ca65997938fff9e5ab6f653e4 +https://conda.anaconda.org/conda-forge/linux-64/chardet-5.2.0-py312h7900ff3_2.conda#01b1679726675bf49851cdb507de4a24 https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda#7f4a9e3fcff3f6356ae99244a014da6a https://conda.anaconda.org/conda-forge/noarch/et_xmlfile-1.1.0-pyhd8ed1ab_0.conda#a2f2138597905eaa72e561d8efb42cf3 https://conda.anaconda.org/conda-forge/linux-64/frozenlist-1.4.1-py312h98912ed_0.conda#2715764dfa5fb00343e03d5a59b64582 -https://conda.anaconda.org/conda-forge/noarch/idna-3.7-pyhd8ed1ab_0.conda#c0cc1420498b17414d8617d0b9f506ca -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8 +https://conda.anaconda.org/conda-forge/noarch/hpack-4.0.0-pyh9f0ad1d_0.tar.bz2#914d6646c4dbb1fd3ff539830a12fd71 +https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_0.tar.bz2#9f765cbfab6870c8435b9eefecd7a1f4 +https://conda.anaconda.org/conda-forge/noarch/idna-3.8-pyhd8ed1ab_0.conda#99e164522f6bdf23c177c8d9ae63f975 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c https://conda.anaconda.org/conda-forge/noarch/mpmath-1.3.0-pyhd8ed1ab_0.conda#dbf6e2d89137da32fa6670f3bffc024e https://conda.anaconda.org/conda-forge/linux-64/multidict-6.0.5-py312h98912ed_0.conda#d0d2cab29d6c33c47f719d7a1879e08b https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.6.0-pyhd8ed1ab_0.conda#6598c056f64dc8800d40add25e4e2c34 -https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.8-py312h98912ed_0.conda#3facaca6cc0f7988df3250efccd32da3 +https://conda.anaconda.org/conda-forge/linux-64/psutil-6.0.0-py312h9a8786e_0.conda#1aeffa86c55972ca4e88ac843eccedf2 +https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda#844d9eb3b43095b031874477f7d70088 https://conda.anaconda.org/bioconda/noarch/pyliftover-0.4-py_0.tar.bz2#9b2bbe0d19a100347893215e56dd1133 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+https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.0-py312h1103770_0.conda#9709027e8a51a3476db65a3c0cf806c2 +https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py312h3483029_0.conda#eab52e88c858d87cf5a069f79d10bb50 +https://conda.anaconda.org/conda-forge/linux-64/biopython-1.84-py312h9a8786e_0.conda#6683d74a08fc106ef44d6ac403dc7aee +https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.2-pyhd8ed1ab_1.conda#e804c43f58255e977093a2298e442bb8 https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda#5ede4753180c7a550a443c430dc8ab52 -https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py312h98912ed_0.conda#53e12da7730d109fddca08aef28a4a50 https://conda.anaconda.org/conda-forge/noarch/requests-toolbelt-1.0.0-pyhd8ed1ab_0.conda#99c98318c8646b08cc764f90ce98906e -https://conda.anaconda.org/bioconda/noarch/open-cravat-2.7.3-pyhdfd78af_0.tar.bz2#a61c53c5da5dee287c9ef4fdcf4416bb +https://conda.anaconda.org/bioconda/noarch/open-cravat-2.8.0-pyhdfd78af_0.tar.bz2#b1910703d441f8d5ce958e0f12b9e084 diff --git a/bio/open-cravat/module/environment.yaml b/bio/open-cravat/module/environment.yaml index 82a282c33d..eef99a791f 100644 --- a/bio/open-cravat/module/environment.yaml +++ b/bio/open-cravat/module/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - open-cravat =2.7.3 + - open-cravat =2.8.0 diff --git a/bio/open-cravat/run/environment.linux-64.pin.txt b/bio/open-cravat/run/environment.linux-64.pin.txt index a0984dd608..661db40d47 100644 --- a/bio/open-cravat/run/environment.linux-64.pin.txt +++ b/bio/open-cravat/run/environment.linux-64.pin.txt @@ -3,73 +3,84 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_1.conda#10a0cef64b784d6ab6da50ebca4e984d +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h3d2ce59_11.conda#c485da4fdb454539f852a90ae06e9bb7 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.1.0-h69a702a_1.conda#591e631bc1ae62c64f2ab4f66178c097 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_11.conda#eaa8ea74083fb4a78ae19e431e556003 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b 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-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_11.conda#4c3e460d6acf8e43e4ce8bf405187eb7 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_1.conda#16cec94c5992d7f42ae3f9fa8b25df8d https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155 -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 -https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda#5e4c0743c70186509d1412e03c2d8dfa 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=2.28.0 diff --git a/bio/rasusa/environment.linux-64.pin.txt b/bio/rasusa/environment.linux-64.pin.txt index 1480bce84d..447589cb05 100644 --- a/bio/rasusa/environment.linux-64.pin.txt +++ b/bio/rasusa/environment.linux-64.pin.txt @@ -3,7 +3,8 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978 -https://conda.anaconda.org/bioconda/linux-64/rasusa-2.0.0-h031d066_0.tar.bz2#59ca5054e6ec09ee5e7ec23c8b010a14 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/bioconda/linux-64/rasusa-2.1.0-h715e4b3_0.tar.bz2#ac3a2dee0a6c30e43919a72c949ed0dd diff --git a/bio/rasusa/environment.yaml b/bio/rasusa/environment.yaml index b7847cec46..15bfbad581 100644 --- a/bio/rasusa/environment.yaml +++ b/bio/rasusa/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - rasusa =2.0.0 + - rasusa =2.1.0 diff --git a/bio/rseqc/bam_stat/environment.linux-64.pin.txt b/bio/rseqc/bam_stat/environment.linux-64.pin.txt new file mode 100644 index 0000000000..16d6ce335c --- /dev/null +++ b/bio/rseqc/bam_stat/environment.linux-64.pin.txt @@ -0,0 +1,111 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f 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+https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.22-py312hfa7e9eb_3.tar.bz2#47368e260acfd3e3bef48698587d9c17 +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.4.1-h518d376_15.conda#546e03ae83233024b52dedce484e0baf +https://conda.anaconda.org/bioconda/linux-64/rseqc-5.0.3-py312hf67a6ed_2.tar.bz2#f9e09df66a66558ecb4d815d5da50cc2 diff --git a/bio/rseqc/bam_stat/environment.yaml b/bio/rseqc/bam_stat/environment.yaml new file mode 100644 index 0000000000..79284140d2 --- /dev/null +++ b/bio/rseqc/bam_stat/environment.yaml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - rseqc =5.0.3 diff --git a/bio/rseqc/bam_stat/meta.yaml b/bio/rseqc/bam_stat/meta.yaml new file mode 100644 index 0000000000..9a76d79027 --- /dev/null +++ b/bio/rseqc/bam_stat/meta.yaml @@ -0,0 +1,14 @@ +name: RSeQC bam_stat.py +url: https://rseqc.sourceforge.net/#bam-stat-py +description: > + Summarizing mapping statistics of a BAM or SAM file. +authors: + - Thibault Dayris +input: + - Path to BAM/SAM file(s) to summarize. +output: + - Path to summary +params: + - extra: Optional argument basides `--input-file` +notes: > + Only mapping quality can be provided as optional parameters, since `--help` and `--version` do not produce summary. diff --git a/bio/rseqc/bam_stat/test/Snakefile b/bio/rseqc/bam_stat/test/Snakefile new file mode 100644 index 0000000000..01a36dd3f5 --- /dev/null +++ b/bio/rseqc/bam_stat/test/Snakefile @@ -0,0 +1,12 @@ +rule test_rseqc_bam_stat: + input: + "a.bam", + output: + "a.stats", + threads: 1 + params: + extra="--mapq 5", + log: + "bastat.log", + wrapper: + "master/bio/rseqc/bam_stat" diff --git a/bio/rseqc/bam_stat/test/a.bam b/bio/rseqc/bam_stat/test/a.bam new file mode 100644 index 0000000000..42f4bdd54f Binary files /dev/null and b/bio/rseqc/bam_stat/test/a.bam differ diff --git a/bio/rseqc/bam_stat/test/a.bam.bai b/bio/rseqc/bam_stat/test/a.bam.bai new file mode 100644 index 0000000000..e2e66bf0a7 Binary files /dev/null and b/bio/rseqc/bam_stat/test/a.bam.bai differ diff --git a/bio/rseqc/bam_stat/wrapper.py b/bio/rseqc/bam_stat/wrapper.py new file mode 100644 index 0000000000..b45bc57f5c --- /dev/null +++ b/bio/rseqc/bam_stat/wrapper.py @@ -0,0 +1,13 @@ +# coding: utf-8 + +__author__ = "Thibault Dayris" +__mail__ = "thibault.dayris@gustaveroussy.fr" +__copyright__ = "Copyright 2024, Thibault Dayris" +__license__ = "MIT" + +from snakemake import shell + +extra = snakemake.params.get("extra", "") +log = snakemake.log_fmt_shell(stdout=False, stderr=True) + +shell("bam_stat.py --input-file {snakemake.input[0]} > {snakemake.output} {log}") diff --git a/bio/rseqc/inner_distance/environment.linux-64.pin.txt b/bio/rseqc/inner_distance/environment.linux-64.pin.txt new file mode 100644 index 0000000000..6e7a89ce6c --- /dev/null +++ b/bio/rseqc/inner_distance/environment.linux-64.pin.txt @@ -0,0 +1,107 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# 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+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb +https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f907bb958910dc404647326ca80c263e +https://conda.anaconda.org/conda-forge/linux-64/curl-8.7.1-hca28451_0.conda#d2dd5466be2ce818f8097847341da63d +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-21_linux64_openblas.conda#4a3816d06451c4946e2db26b86472cb6 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-21_linux64_openblas.conda#1a42f305615c3867684e049e85927531 +https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.0-py310h41dec4a_1.tar.bz2#19fdb9301a6debbb7fe9836670e3feb7 +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.3.0-h3d44ed6_0.conda#5a6f6c00ef982a9bc83558d9ac8f64a0 +https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be +https://conda.anaconda.org/bioconda/linux-64/bx-python-0.11.0-py310h551a815_1.tar.bz2#480263b53dc93059dd55b452709e6777 +https://conda.anaconda.org/conda-forge/linux-64/pango-1.50.14-ha41ecd1_2.conda#1a66c10f6a0da3dbd2f3a68127e7f6a0 +https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.22-py310h79000e5_2.tar.bz2#9021f57dc4044c4b61619ac2c24e29d8 +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.1-h639d9d3_5.conda#f320a6b4aba89a080d757a365138b642 +https://conda.anaconda.org/bioconda/linux-64/rseqc-5.0.3-py310h4b81fae_0.tar.bz2#00cae15f53e968ef03166df3e464b4c6 diff --git a/bio/rseqc/inner_distance/environment.yaml b/bio/rseqc/inner_distance/environment.yaml new file mode 100644 index 0000000000..4c767e6325 --- /dev/null +++ b/bio/rseqc/inner_distance/environment.yaml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - rseqc=5.0.3 diff --git a/bio/rseqc/inner_distance/meta.yaml b/bio/rseqc/inner_distance/meta.yaml new file mode 100644 index 0000000000..0b6366fe77 --- /dev/null +++ b/bio/rseqc/inner_distance/meta.yaml @@ -0,0 +1,15 @@ +name: inner_distance +description: Calculate inner distance between read pairs +url: "https://rseqc.sourceforge.net/#inner-distance-py" +authors: + - "Thibault Dayris" +input: + - aln: Path to SAM/BAM input + - refgene: Path to refgene model +output: + - reads_inner_distance: Optional path to per-read inner distance table + - pdf: Optional path to pdf graph + - plot_r: Optional Path to R script + - freq: Optional path to inner distance frequence +params: + - extra: Optional parameters for `inner_distance.py`, besides `-i`, `-r`, or `-o` diff --git a/bio/rseqc/inner_distance/test/A.bam b/bio/rseqc/inner_distance/test/A.bam new file mode 100644 index 0000000000..57511ab353 Binary files /dev/null and b/bio/rseqc/inner_distance/test/A.bam differ diff --git a/bio/rseqc/inner_distance/test/Snakefile b/bio/rseqc/inner_distance/test/Snakefile new file mode 100644 index 0000000000..acff6a4e9a --- /dev/null +++ b/bio/rseqc/inner_distance/test/Snakefile @@ -0,0 +1,15 @@ +rule test_rseqc_inner_distance: + input: + aln="A.bam", + refgene="annotation.bed", + output: + reads_inner_distance="a.txt", + freq="freq.txt", + pdf="a.pdf", + plot_r="script.a.r", + log: + "rseqc.log", + params: + extra="-k3 -q2", + wrapper: + "master/bio/rseqc/inner_distance" diff --git a/bio/rseqc/inner_distance/test/annotation.bed b/bio/rseqc/inner_distance/test/annotation.bed new file mode 100644 index 0000000000..393b43a740 --- /dev/null +++ b/bio/rseqc/inner_distance/test/annotation.bed @@ -0,0 +1,2 @@ +1 0 80 ENST00000000000 0 + 80 80 0 1 80, 0, +2 0 80 ENST00000000001 0 + 80 80 0 1 80, 0, diff --git a/bio/rseqc/inner_distance/wrapper.py b/bio/rseqc/inner_distance/wrapper.py new file mode 100644 index 0000000000..e4980f8ac2 --- /dev/null +++ b/bio/rseqc/inner_distance/wrapper.py @@ -0,0 +1,51 @@ +# coding: utf-8 + +"""Snakemake wrapper for RSeQC inner_distance.py""" + +__author__ = "Thibault Dayris" +__mail__ = "thibault.dayris@gustaveroussy.fr" +__copyright__ = "Copyright 2024, Thibault Dayris" +__license__ = "MIT" + +from tempfile import TemporaryDirectory +from snakemake import shell + +extra = snakemake.params.get("extra", "") +log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True) + +with TemporaryDirectory() as tempdir: + shell( + "inner_distance.py {extra} " + "--input-file {snakemake.input.aln} " + "--refgene {snakemake.input.refgene} " + "--out-prefix {tempdir}/out " + "{log} " + ) + + if snakemake.output.get("reads_inner_distance"): + shell( + "mv --verbose " + "{tempdir}/out.inner_distance.txt " + "{snakemake.output.reads_inner_distance} {log}" + ) + + if snakemake.output.get("pdf"): + shell( + "mv --verbose " + "{tempdir}/out.inner_distance_plot.pdf " + "{snakemake.output.pdf} {log}" + ) + + if snakemake.output.get("freq"): + shell( + "mv --verbose " + "{tempdir}/out.inner_distance_freq.txt " + "{snakemake.output.freq} {log}" + ) + + if snakemake.output.get("plot_r"): + shell( + "mv --verbose " + "{tempdir}/out.inner_distance_plot.r " + "{snakemake.output.plot_r} {log}" + ) diff --git a/bio/seqkit/test/Snakefile b/bio/seqkit/test/Snakefile index 6e41279596..2569e8e32f 100644 --- a/bio/seqkit/test/Snakefile +++ b/bio/seqkit/test/Snakefile @@ -153,3 +153,39 @@ rule seqkit_stats: threads: 2 wrapper: "master/bio/seqkit" + + +rule seqkit_common: + input: + fastas=[ + "data/{sample1}.fa", + "data/{sample2}.fa", + ], + output: + fasta="out/common/{sample1}_{sample2}.fa.gz", + log: + "logs/common/{sample1}_{sample2}.log", + params: + command="common", + extra="", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_concat: + input: + fastas=[ + "data/{sample1}.fa", + "data/{sample2}.fa", + ], + output: + fasta="out/concat/{sample1}_{sample2}.fa.gz", + log: + "logs/concat/{sample1}_{sample2}.log", + params: + command="concat", + extra="", + threads: 2 + wrapper: + "master/bio/seqkit" diff --git a/bio/seqkit/test/data/b.fa b/bio/seqkit/test/data/b.fa new file mode 100644 index 0000000000..69217659d3 --- /dev/null +++ b/bio/seqkit/test/data/b.fa @@ -0,0 +1,4 @@ +>seq1 +tgACTGac +>seq3 +actg \ No newline at end of file diff --git a/bio/seqkit/wrapper.py b/bio/seqkit/wrapper.py index 21eb433d46..935850f6d0 100644 --- a/bio/seqkit/wrapper.py +++ b/bio/seqkit/wrapper.py @@ -8,6 +8,11 @@ extra = snakemake.params.get("extra", "") log = snakemake.log_fmt_shell(stdout=True, stderr=True) +# subcommands concat and common use multiple input files +if snakemake.params.command in ["concat", "common"]: + input = " ".join(snakemake.input) +else: + input = snakemake.input[0] extra_input = " ".join( [ @@ -39,6 +44,6 @@ " {extra_output}" " {extra}" " --out-file {snakemake.output[0]}" - " {snakemake.input[0]}" + " {input}" " {log}" ) diff --git a/bio/ucsc/bedGraphToBigWig/environment.linux-64.pin.txt b/bio/ucsc/bedGraphToBigWig/environment.linux-64.pin.txt index b0a5e7d84a..0e6ece9434 100644 --- a/bio/ucsc/bedGraphToBigWig/environment.linux-64.pin.txt +++ b/bio/ucsc/bedGraphToBigWig/environment.linux-64.pin.txt @@ -3,14 +3,18 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.0-hd590300_1.conda#603827b39ea2b835268adb8c821b8570 -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda#e1c890aebdebbfbf87e2c917187b4416 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a +https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.3.1-hb9d3cd8_3.conda#35e3d362673fd1d937664c1dbe76879b +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe -https://conda.anaconda.org/bioconda/linux-64/ucsc-bedgraphtobigwig-455-h2a80c09_0.tar.bz2#f14b9133266860fb70b681fc978099ae +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/bioconda/linux-64/ucsc-bedgraphtobigwig-469-h9b8f530_0.tar.bz2#882d161cbee36300ca3995e920fdcfa2 diff --git a/bio/ucsc/bedGraphToBigWig/environment.yaml b/bio/ucsc/bedGraphToBigWig/environment.yaml index 5ebe4f2800..337a960acc 100644 --- a/bio/ucsc/bedGraphToBigWig/environment.yaml +++ b/bio/ucsc/bedGraphToBigWig/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - ucsc-bedgraphtobigwig =455 + - ucsc-bedgraphtobigwig =469 diff --git a/bio/ucsc/faToTwoBit/environment.linux-64.pin.txt b/bio/ucsc/faToTwoBit/environment.linux-64.pin.txt index 7d012020b6..40bc3a9e11 100644 --- a/bio/ucsc/faToTwoBit/environment.linux-64.pin.txt +++ b/bio/ucsc/faToTwoBit/environment.linux-64.pin.txt @@ -3,14 +3,18 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.4-hd590300_0.conda#412ba6938c3e2abaca8b1129ea82e238 -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda#e1c890aebdebbfbf87e2c917187b4416 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a +https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.3.1-hb9d3cd8_3.conda#35e3d362673fd1d937664c1dbe76879b +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe -https://conda.anaconda.org/bioconda/linux-64/ucsc-fatotwobit-455-h2a80c09_0.tar.bz2#86ec1cfa613092b36c00a29a24a7dd66 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/bioconda/linux-64/ucsc-fatotwobit-469-he8037a5_2.tar.bz2#cc88bb00b3c5cdac9c9881e4bbcdeb0e diff --git a/bio/ucsc/faToTwoBit/environment.yaml b/bio/ucsc/faToTwoBit/environment.yaml index 7dc7bcea94..89f964b81d 100644 --- a/bio/ucsc/faToTwoBit/environment.yaml +++ b/bio/ucsc/faToTwoBit/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - ucsc-fatotwobit =455 + - ucsc-fatotwobit =469 diff --git a/bio/ucsc/genePredToBed/environment.linux-64.pin.txt b/bio/ucsc/genePredToBed/environment.linux-64.pin.txt index 0dccb6d2b9..8beb30a1ce 100644 --- a/bio/ucsc/genePredToBed/environment.linux-64.pin.txt +++ b/bio/ucsc/genePredToBed/environment.linux-64.pin.txt @@ -3,14 +3,18 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1w-hd590300_0.conda#301e70057a3bd399640bb16bbdf87995 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a +https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.3.1-hb9d3cd8_3.conda#35e3d362673fd1d937664c1dbe76879b https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae -https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h6eb9d5d_1007.tar.bz2#10300d974fbd414ed703be7ac9870c18 -https://conda.anaconda.org/bioconda/linux-64/ucsc-genepredtobed-447-h954228d_0.tar.bz2#71adc6b3d2ab0c3d29b21042ff6a039b +https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/bioconda/linux-64/ucsc-genepredtobed-469-h9b8f530_0.tar.bz2#ceaff7689880bfcdef92e21f61431679 diff --git a/bio/ucsc/genePredToBed/environment.yaml b/bio/ucsc/genePredToBed/environment.yaml index 7d59b19fc0..2a2a07fe94 100644 --- a/bio/ucsc/genePredToBed/environment.yaml +++ b/bio/ucsc/genePredToBed/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - ucsc-genepredtobed =447 + - ucsc-genepredtobed =469 diff --git a/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt b/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt index 207e796cff..9737532ffb 100644 --- a/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt +++ b/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt @@ -5,30 +5,34 @@ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 +https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.3.1-hb9d3cd8_3.conda#35e3d362673fd1d937664c1dbe76879b https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84 -https://conda.anaconda.org/bioconda/linux-64/ucsc-gtftogenepred-447-h2a80c09_1.tar.bz2#ce9b02e8731a0e7bc826f0c71c2e356a +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 +https://conda.anaconda.org/bioconda/linux-64/ucsc-gtftogenepred-469-h9b8f530_0.tar.bz2#f0f9a2a702f66e75edafc4f67fdde693 https://conda.anaconda.org/conda-forge/noarch/dbfread-2.0.7-py_0.tar.bz2#710b599a886746c5f4211818a15f6ab6 https://conda.anaconda.org/conda-forge/noarch/et_xmlfile-1.1.0-pyhd8ed1ab_0.conda#a2f2138597905eaa72e561d8efb42cf3 https://conda.anaconda.org/conda-forge/noarch/future-1.0.0-pyhd8ed1ab_0.conda#650a7807e689642dddd3590eb817beed @@ -37,22 +41,22 @@ https://conda.anaconda.org/conda-forge/noarch/parsedatetime-2.4-py_1.tar.bz2#8df https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda#844d9eb3b43095b031874477f7d70088 https://conda.anaconda.org/conda-forge/noarch/pytimeparse-1.1.8-py_0.tar.bz2#edde7e7260599f9860002187486b3e01 https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad -https://conda.anaconda.org/conda-forge/noarch/setuptools-71.0.4-pyhd8ed1ab_0.conda#ee78ac9c720d0d02fcfd420866b82ab1 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/text-unidecode-1.3-pyhd8ed1ab_1.conda#ba8aba332d8868897ce44ad74015a7fe -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 https://conda.anaconda.org/conda-forge/noarch/xlrd-2.0.1-pyhd8ed1ab_3.tar.bz2#97dfcd5ff030d829b55f67e82f928093 https://conda.anaconda.org/conda-forge/noarch/babel-2.14.0-pyhd8ed1ab_0.conda#9669586875baeced8fc30c0826c3270e -https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py312hf06ca03_0.conda#56b0ca764ce23cc54f3f7e2a7b970f6d +https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.0-py312h06ac9bb_1.conda#db9bdbaee0f524ead0471689f002781e https://conda.anaconda.org/conda-forge/noarch/isodate-0.6.1-pyhd8ed1ab_0.tar.bz2#4a62c93c1b5c0b920508ae3fd285eaf5 https://conda.anaconda.org/conda-forge/noarch/leather-0.3.4-pyhd8ed1ab_0.tar.bz2#513f26ec3c158a325b16df2da418df82 -https://conda.anaconda.org/conda-forge/linux-64/openpyxl-3.1.4-py312h98912ed_0.conda#678227a6922230b10dbf93b8d161c38d -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/linux-64/openpyxl-3.1.5-py312h98912ed_0.conda#5265c8fb3517b52a39bf253387d35dcf +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyh8b19718_1.conda#6c78fbb8ddfd64bcb55b5cbafd2d2c43 https://conda.anaconda.org/conda-forge/noarch/python-slugify-8.0.4-pyhd8ed1ab_0.conda#4b11845622b3c3178c0e989235b53975 https://conda.anaconda.org/conda-forge/linux-64/sqlalchemy-1.4.49-py312h98912ed_1.conda#755a7fbdcbf783fe197b2367ed944f86 https://conda.anaconda.org/conda-forge/linux-64/cld2-cffi-0.1.4-py312h30efb56_1005.conda#3a8ba4ad9ab365e3cbe610819f206603 https://conda.anaconda.org/conda-forge/linux-64/pyicu-2.13.1-py312h5c10c66_1.conda#d0ba0a8a2fe1324ce74475b5a32e3cd8 -https://conda.anaconda.org/conda-forge/noarch/agate-1.11.0-pyh707e725_0.conda#65a4cc6ffe639ccecb6a4341950d240e +https://conda.anaconda.org/conda-forge/noarch/agate-1.12.0-pyh707e725_0.conda#8d2755bc81e4ad0af797169ee9f4bae3 https://conda.anaconda.org/conda-forge/noarch/agate-dbf-0.2.3-pyhd8ed1ab_0.conda#9e33e31e72d8bbe2d96b49c9a534ba2f https://conda.anaconda.org/conda-forge/noarch/agate-excel-0.2.3-py_0.tar.bz2#26a3416153f17addfdab82a183665a98 https://conda.anaconda.org/conda-forge/noarch/agate-sql-0.7.2-pyhd8ed1ab_0.conda#6279859d84efb3bf26ccd89b47278711 diff --git a/bio/ucsc/gtfToGenePred/environment.yaml b/bio/ucsc/gtfToGenePred/environment.yaml index 3e3a698026..ba7f3ebbcd 100644 --- a/bio/ucsc/gtfToGenePred/environment.yaml +++ b/bio/ucsc/gtfToGenePred/environment.yaml @@ -3,5 +3,5 @@ channels: - bioconda - nodefaults dependencies: - - ucsc-gtftogenepred =447 + - ucsc-gtftogenepred =469 - csvkit =2.0.1 diff --git a/bio/ucsc/twoBitInfo/environment.linux-64.pin.txt b/bio/ucsc/twoBitInfo/environment.linux-64.pin.txt index 5b4ffa6e25..2aae8c0e17 100644 --- a/bio/ucsc/twoBitInfo/environment.linux-64.pin.txt +++ b/bio/ucsc/twoBitInfo/environment.linux-64.pin.txt @@ -3,14 +3,18 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.0-hd590300_1.conda#603827b39ea2b835268adb8c821b8570 -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda#e1c890aebdebbfbf87e2c917187b4416 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a +https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.3.1-hb9d3cd8_3.conda#35e3d362673fd1d937664c1dbe76879b +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe -https://conda.anaconda.org/bioconda/linux-64/ucsc-twobitinfo-455-h2a80c09_0.tar.bz2#b1e43746787a507992e8a4b44ea90db0 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/bioconda/linux-64/ucsc-twobitinfo-469-h9b8f530_0.tar.bz2#e58423271bf83b344ae4503246f50eae diff --git a/bio/ucsc/twoBitInfo/environment.yaml b/bio/ucsc/twoBitInfo/environment.yaml index 49f288a0cf..fa9b54ff20 100644 --- a/bio/ucsc/twoBitInfo/environment.yaml +++ b/bio/ucsc/twoBitInfo/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - ucsc-twobitinfo =455 + - ucsc-twobitinfo =469 diff --git a/bio/ucsc/twoBitToFa/environment.linux-64.pin.txt b/bio/ucsc/twoBitToFa/environment.linux-64.pin.txt index 76c154be36..68cf5e0a2a 100644 --- a/bio/ucsc/twoBitToFa/environment.linux-64.pin.txt +++ b/bio/ucsc/twoBitToFa/environment.linux-64.pin.txt @@ -3,14 +3,18 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-h4852527_1.conda#bd2598399a70bb86d8218e95548d735e https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.4-hd590300_0.conda#412ba6938c3e2abaca8b1129ea82e238 -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda#e1c890aebdebbfbf87e2c917187b4416 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a +https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.3.1-hb9d3cd8_3.conda#35e3d362673fd1d937664c1dbe76879b +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe -https://conda.anaconda.org/bioconda/linux-64/ucsc-twobittofa-455-h2a80c09_0.tar.bz2#bd8671f0c567aee0b41abf6b256f588a +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/bioconda/linux-64/ucsc-twobittofa-469-h9b8f530_0.tar.bz2#62be01088bc15719e043b5de16637fa8 diff --git a/bio/ucsc/twoBitToFa/environment.yaml b/bio/ucsc/twoBitToFa/environment.yaml index e50086b0dc..72f43c5f51 100644 --- a/bio/ucsc/twoBitToFa/environment.yaml +++ b/bio/ucsc/twoBitToFa/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - ucsc-twobittofa =455 + - ucsc-twobittofa =469 diff --git a/test.py b/test.py index 5b94f6738b..57c158f4d3 100644 --- a/test.py +++ b/test.py @@ -429,6 +429,36 @@ def test_seqkit_seq(): ) +@skip_if_not_modified +def test_seqkit_common(): + run( + "bio/seqkit", + [ + "snakemake", + "--cores", + "2", + "--use-conda", + "-F", + "out/common/a_b.fa.gz", + ], + ) + + +@skip_if_not_modified +def test_seqkit_concat(): + run( + "bio/seqkit", + [ + "snakemake", + "--cores", + "2", + "--use-conda", + "-F", + "out/concat/a_b.fa.gz", + ], + ) + + @skip_if_not_modified def test_sickle_pe(): run( @@ -2865,6 +2895,21 @@ def test_deeptools_computematrix(): ) +@skip_if_not_modified +def test_deeptools_plotcorrelation(): + run( + "bio/deeptools/plotcorrelation", + [ + "snakemake", + "--cores", + "1", + "bins.svg", + "--use-conda", + "-F" + ], + ) + + @skip_if_not_modified def test_deeptools_bamcoverage(): run( @@ -2880,6 +2925,32 @@ def test_deeptools_bamcoverage(): ) +@skip_if_not_modified +def test_deeptools_multibigwigsummary(): + run( + "bio/deeptools/multibigwigsummary", + [ + "snakemake", + "--cores", + "1", + "--use-conda", + "-F", + "bins.npz", + ], + ) + run( + "bio/deeptools/multibigwigsummary", + [ + "snakemake", + "--cores", + "1", + "--use-conda", + "-F", + "bed.npz", + ], + ) + + @skip_if_not_modified def test_deeptools_bamcoverage_eff(): run( @@ -2924,6 +2995,20 @@ def test_deeptools_alignmentsieve(): ], ) +@skip_if_not_modified +def test_deeptools_plot_pca(): + run( + "bio/deeptools/plotpca", + [ + "snakemake", + "--cores", + "1", + "pca.svg", + "--use-conda", + "-F", + ], + ) + @skip_if_not_modified def test_deeptools_plotheatmap(): @@ -6458,6 +6543,14 @@ def test_generate_data_matrix(): ) +@skip_if_not_modified +def test_rseqc_inner_distance(): + run( + "bio/rseqc/inner_distance", + ["snakemake", "--cores", "1", "--use-conda", "-F", "a.pdf"], + ) + + @skip_if_not_modified def test_rseqc_infer_experiment(): run( @@ -6465,6 +6558,13 @@ def test_rseqc_infer_experiment(): ["snakemake", "--cores", "1", "--use-conda", "-F", "a.experiment.txt"], ) +@skip_if_not_modified +def test_rseqc_bam_stat(): + run( + "bio/rseqc/bam_stat", + ["snakemake", "--cores", "1", "--use-conda", "-F", "a.stats"], + ) + @skip_if_not_modified def test_rseqc_read_gc():