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- bioconda | ||
- nodefaults | ||
dependencies: | ||
- adapterremoval =2.3.3 | ||
- adapterremoval =2.3.4 |
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bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt
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# This file may be used to create an environment using: | ||
# $ conda create --name <env> --file <this 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 | ||
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda#51a753e64a3027bd7e23a189b1f6e91e | ||
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 | ||
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/libbrotlidec-1.1.0-hd590300_1.conda#f07002e225d7a60a694d42a7bf5ff53f | ||
https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hd590300_1.conda#5fc11c6020d421960607d821310fcd4d | ||
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/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a | ||
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-3.45.2-h2797004_0.conda#866983a220e27a80cb75e85cb30466a1 | ||
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe | ||
https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda#33277193f5b92bad9fdd230eb700929c | ||
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/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda#39f910d205726805a958da408ca194ba | ||
https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb | ||
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-0.3.26-pthreads_h413a1c8_0.conda#760ae35415f5ba8b15d09df5afe8b23a | ||
https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h8b53f26_0.conda#097c175e54beba8b42dcc5dd49299ca1 | ||
https://conda.anaconda.org/conda-forge/linux-64/python-3.10.13-hd12c33a_1_cpython.conda#ed38140af93f81319ebc472fbcf16cca | ||
https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda#def531a3ac77b7fb8c21d17bb5d0badb | ||
https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hd590300_1.conda#f27a24d46e3ea7b70a1f98e50c62508f | ||
https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py310hc6cd4ac_1.conda#1f95722c94f00b69af69a066c7433714 | ||
https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333 | ||
https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda#7f4a9e3fcff3f6356ae99244a014da6a | ||
https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2#3faab06a954c2a04039983f2c4a50d99 | ||
https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441 | ||
https://conda.anaconda.org/bioconda/linux-64/deeptoolsintervals-0.1.9-py310h8472f5a_7.tar.bz2#744fef3bf2b60be8817fc1cf92cb3d28 | ||
https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20.1-py310hff52083_3.conda#c159dcd29bbd80b187b1c5d5f73cc971 | ||
https://conda.anaconda.org/conda-forge/noarch/idna-3.6-pyhd8ed1ab_0.conda#1a76f09108576397c41c0b0c5bd84134 | ||
https://conda.anaconda.org/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.bz2#7de5386c8fea29e76b303f37dde4c352 | ||
https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.5-py310hd41b1e2_1.conda#b8d67603d43b23ce7e988a5d81a7ab79 | ||
https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.15-h7f713cb_2.conda#9ab79924a3760f85a799f21bc99bd655 | ||
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-21_linux64_openblas.conda#0ac9f44fc096772b0aa092119b00c3ca | ||
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb | ||
https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.5-py310h2372a71_0.conda#f6703fa0214a00bf49d1bef6dc7672d0 | ||
https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyh9f0ad1d_0.tar.bz2#2ba8498c1018c1e9c61eb99b973dfe19 | ||
https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda#7f2e286780f072ed750df46dc2631138 | ||
https://conda.anaconda.org/conda-forge/noarch/packaging-24.0-pyhd8ed1ab_0.conda#248f521b64ce055e7feae3105e7abeb8 | ||
https://conda.anaconda.org/bioconda/linux-64/py2bit-0.3.0-py310h4b81fae_8.tar.bz2#9ed0a68028d591c315ad4199964df81c | ||
https://conda.anaconda.org/conda-forge/noarch/pygments-2.17.2-pyhd8ed1ab_0.conda#140a7f159396547e9799aa98f9f0742e | ||
https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.1.2-pyhd8ed1ab_0.conda#b9a4dacf97241704529131a0dfc0494f | ||
https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2#2a7de29fb590ca14b5243c4c812c8025 | ||
https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad | ||
https://conda.anaconda.org/conda-forge/noarch/setuptools-69.2.0-pyhd8ed1ab_0.conda#da214ecd521a720a9d521c68047682dc | ||
https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 | ||
https://conda.anaconda.org/conda-forge/noarch/snowballstemmer-2.2.0-pyhd8ed1ab_0.tar.bz2#4d22a9315e78c6827f806065957d566e | ||
https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_0.conda#da1d979339e2714c30a8e806a33ec087 | ||
https://conda.anaconda.org/conda-forge/noarch/tabulate-0.9.0-pyhd8ed1ab_1.tar.bz2#4759805cce2d914c38472f70bf4d8bcb | ||
https://conda.anaconda.org/conda-forge/noarch/tenacity-8.2.3-pyhd8ed1ab_0.conda#1482e77f87c6a702a7e05ef22c9b197b | ||
https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-15.1.0-py310h2372a71_0.conda#72637c58d36d9475fda24700c9796f19 | ||
https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda#1cdea58981c5cbc17b51973bcaddcea7 | ||
https://conda.anaconda.org/conda-forge/noarch/zipp-3.17.0-pyhd8ed1ab_0.conda#2e4d6bc0b14e10f895fc6791a7d9b26a | ||
https://conda.anaconda.org/conda-forge/noarch/babel-2.14.0-pyhd8ed1ab_0.conda#9669586875baeced8fc30c0826c3270e | ||
https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.49.0-py310h2372a71_0.conda#e61ae80fde506b70a88e5e06376d2068 | ||
https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.0.2-pyha770c72_0.conda#b050a4bb0e90ebd6e7fa4093d6346867 | ||
https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.3-pyhd8ed1ab_0.conda#e7d8df6509ba635247ff9aea31134262 | ||
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/linux-64/pillow-10.0.1-py310h29da1c1_1.conda#8e93b1c69cddf89fd412178d3d418bae | ||
https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 | ||
https://conda.anaconda.org/conda-forge/noarch/plotly-5.19.0-pyhd8ed1ab_0.conda#669cd7065794633b9e64e6a9612ec700 | ||
https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.0-py310h41dec4a_1.tar.bz2#19fdb9301a6debbb7fe9836670e3feb7 | ||
https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c | ||
https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.1-pyhd8ed1ab_0.conda#08807a87fa7af10754d46f63b368e016 | ||
https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be | ||
https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda#a30144e4156cdbb236f99ebb49828f8b | ||
https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.0-py310hd41b1e2_0.conda#85d2aaa7af046528d339da1e813c3a9f | ||
https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.22-py310h79000e5_1.tar.bz2#d76b604c9fba498cb505397e2ec85485 | ||
https://conda.anaconda.org/conda-forge/linux-64/scipy-1.12.0-py310hb13e2d6_2.conda#cd3baec470071490bc5ab05da64c52b5 | ||
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 |
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channels: | ||
- conda-forge | ||
- bioconda | ||
- nodefaults | ||
dependencies: | ||
- deeptools =3.5.5 |
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name: deeptools multi bigwig summary | ||
url: 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. |
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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" | ||
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||
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" | ||
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# coding: utf-8 | ||
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__author__ = "Thibault Dayris" | ||
__copyright__ = "Copyright 2024, Thibault Dayris" | ||
__email__ = "[email protected]" | ||
__license__ = "MIT" | ||
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from snakemake.shell import shell | ||
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# Optional parameters | ||
log = snakemake.log_fmt_shell(stdout=True, stderr=True) | ||
extra = snakemake.params.get("extra", "") | ||
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blacklist = snakemake.input.get("blacklist") | ||
if blacklist: | ||
extra += f" --blackListFileName {blacklist} " | ||
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out_raw_counts = snakemake.output.get("counts") | ||
if out_raw_counts: | ||
extra += f" --outRawCounts {out_raw_counts} " | ||
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bed = snakemake.input.get("bed") | ||
subcommand = "bins" | ||
if bed: | ||
subcommand = "BED-file" | ||
extra += f" --BED {bed} " | ||
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shell( | ||
"multiBigwigSummary {subcommand} " | ||
"--bwfiles {snakemake.input.bw} " | ||
"--outFileName {snakemake.output.npz} " | ||
"--numberOfProcessors {snakemake.threads} " | ||
"{extra} {log}" | ||
) |
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