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Adding additional deps to dockerfile
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,23 @@ | ||
| # Base image for SQANTI3, | ||
| # Base image for SQANTI3/v5.1.2, | ||
| # uses Ubuntu Jammy (LTS) | ||
| FROM ubuntu:22.04 | ||
|
|
||
| # Depedencies of SQANTI: | ||
| # - https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation | ||
| # - https://github.com/ConesaLab/SQANTI3/blob/master/SQANTI3.conda_env.yml | ||
| # Overview: | ||
| # - perl # apt-get, installs: 5.34.0-3 | ||
| # - minimap2 # apt-get, installs: 2.24 | ||
| # - kallisto # apt-get, installs: 0.46.2 | ||
| # - samtools # apt-get, installs: 1.13-4 | ||
| # - STAR # from github, installs: 2.7.10b | ||
| # - uLTRA # from pypi: installs: 0.1 | ||
| # - deSALT # from github: https://github.com/ydLiu-HIT/deSALT | ||
| # - bedtools # apt-get, installs: 2.30.0 | ||
| # - gffread # apt-get, installs: 0.12.7-2 | ||
| # - gmap # apt-get, installs: 2021-12-17+ds-1 | ||
| # - seqtk # apt-get, installs: 1.3-2 | ||
| # - R>=3.4 # apt-get, installs: 4.1.2-1 | ||
| # -+ perl # apt-get, installs: 5.34.0-3 | ||
| # -+ minimap2 # apt-get, installs: 2.24 | ||
| # -+ kallisto # apt-get, installs: 0.46.2 | ||
| # -+ samtools # apt-get, installs: 1.13-4 | ||
| # -+ STAR # apt-get, installs: 2.7.10a | ||
| # -+ uLTRA # from pypi: installs: 0.1 | ||
| # -+ deSALT # from github: https://github.com/ydLiu-HIT/deSALT | ||
| # -+ bedtools # apt-get, installs: 2.30.0 | ||
| # -+ gffread # apt-get, installs: 0.12.7-2 | ||
| # -+ gmap # apt-get, installs: 2021-12-17+ds-1 | ||
| # -+ seqtk # apt-get, installs: 1.3-2 | ||
| # -+ R>=3.4 # apt-get, installs: 4.1.2-1 | ||
| # @requires: noiseq # from Bioconductor | ||
| # @requires: busparse # from Bioconductor | ||
| # @requires: biocmanager # from CRAN | ||
|
|
@@ -47,22 +47,22 @@ FROM ubuntu:22.04 | |
| # @requires: stringr # from CRAN | ||
| # @requires: tibble # from CRAN | ||
| # @requires: tidyr # from CRAN | ||
| # - python>3.7 # apt-get, installs: 3.10.4-0 | ||
| # @requires: bx-python # pip install from pypi | ||
| # @requires: biopython # pip install from pypi | ||
| # @requires: bcbio-gff # pip install from pypi | ||
| # @requires: cDNA_Cupcake # pip install from github | ||
| # @requires: Cython # pip install from pypi | ||
| # @requires: numpy # pip install from pypi | ||
| # @requires: pysam # pip install from pypi | ||
| # @requires: pybedtools # pip install from pypi, needs bedtools | ||
| # @requires: psutil # pip install from pypi | ||
| # @requires: pandas # pip install from pypi | ||
| # @requires: scipy # pip install from pypi | ||
| # -+ python>3.7 # apt-get, installs: 3.10.6-1 | ||
| # @requires: bx-python # pip install from pypi | ||
| # @requires: biopython # pip install from pypi | ||
| # @requires: bcbio-gff # pip install from pypi | ||
| # @requires: cDNA_Cupcake # pip install from github | ||
| # @requires: Cython # pip install from pypi | ||
| # @requires: numpy # pip install from pypi | ||
| # @requires: pysam # pip install from pypi | ||
| # @requires: pybedtools # pip install from pypi, needs bedtools | ||
| # @requires: psutil # pip install from pypi | ||
| # @requires: pandas # pip install from pypi | ||
| # @requires: scipy # pip install from pypi | ||
| LABEL maintainer="Skyler Kuhn <[email protected]>" \ | ||
| base_image="ubuntu:22.04" \ | ||
| version="v0.1.0" \ | ||
| software="modr" \ | ||
| software="sqanti3/v5.1.2" \ | ||
| about.summary="SQANTI3: Tool for the Quality Control of Long-Read Defined Transcriptomes" \ | ||
| about.home="https://github.com/ConesaLab/SQANTI3" \ | ||
| about.documentation="https://github.com/ConesaLab/SQANTI3/wiki/" \ | ||
|
|
@@ -85,15 +85,114 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \ | |
| # This section installs system packages | ||
| # required for your project. If you need | ||
| # extra system packages add them here. | ||
| RUN apt-get update \ | ||
| && apt-get -y upgrade \ | ||
| && DEBIAN_FRONTEND=noninteractive apt-get install -y \ | ||
| # bedtools/2.30.0 | ||
| bedtools \ | ||
| build-essential \ | ||
| cmake \ | ||
| cpanminus \ | ||
| curl \ | ||
| gawk \ | ||
| # gffread/0.12.7 | ||
| gffread \ | ||
| git \ | ||
| # gmap/2021-12-17 | ||
| gmap \ | ||
| gzip \ | ||
| # kallisto/0.46.2 | ||
| kallisto \ | ||
| libcurl4-openssl-dev \ | ||
| libssl-dev \ | ||
| libxml2-dev \ | ||
| locales \ | ||
| # minimap2/2.24 | ||
| minimap2 \ | ||
| # perl/5.34.0-3 | ||
| perl \ | ||
| pkg-config \ | ||
| # python/3.10.6 | ||
| python3 \ | ||
| python3-pip \ | ||
| # R/4.1.2-1 | ||
| r-base \ | ||
| # STAR/2.7.10a | ||
| rna-star \ | ||
| # samtools/1.13-4 | ||
| samtools \ | ||
| # seqtk/1.3-2 | ||
| seqtk \ | ||
| wget \ | ||
| zlib1g-dev \ | ||
| && apt-get clean && apt-get purge \ | ||
| && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
|
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||
| # Set the locale | ||
| RUN localedef -i en_US -f UTF-8 en_US.UTF-8 | ||
| # Perl fix issue | ||
| RUN cpanm FindBin Term::ReadLine | ||
|
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||
| ############### INSTALL ################ | ||
| # Install any bioinformatics tools | ||
| # available with apt-get on Ubuntu/22.04 | ||
| ############### MANUAL ################ | ||
| # Install tools from src manually, | ||
| # Installs deSALT/1.5.6 from GitHub: | ||
| # https://github.com/ydLiu-HIT/deSALT/releases/tag/v1.5.6 | ||
| # This tool was created using an older | ||
| # version of GCC that allowed multiple | ||
| # definitions of global variables. | ||
| # We are using GCC/10, which does not | ||
| # allow multiple definitations. Adding | ||
| # -Wl,--allow-multiple-definition | ||
| # to the linker to fix this issue. | ||
| RUN mkdir -p /opt2/desalt/1.5.6/ \ | ||
| && wget https://github.com/ydLiu-HIT/deSALT/archive/refs/tags/v1.5.6.tar.gz -O /opt2/desalt/1.5.6/v1.5.6.tar.gz \ | ||
| && tar -zvxf /opt2/desalt/1.5.6/v1.5.6.tar.gz -C /opt2/desalt/1.5.6/ \ | ||
| && rm -f /opt2/desalt/1.5.6/v1.5.6.tar.gz \ | ||
| && cd /opt2/desalt/1.5.6/deSALT-1.5.6/src/deBGA-master/ \ | ||
| && make CFLAGS="-g -Wall -O2 -Wl,--allow-multiple-definition" \ | ||
| && cd .. \ | ||
| && make CFLAGS="-g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function -Wl,--allow-multiple-definition" | ||
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| ENV PATH="${PATH}:/opt2/desalt/1.5.6/deSALT-1.5.6/src" | ||
| WORKDIR /opt2 | ||
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| ############### MANUAL ################ | ||
| # Install tools from src manually | ||
| # Installs namfinder, requirement of | ||
| # ultra-bioinformatics tool from pypi. | ||
| RUN mkdir -p /opt2/namfinder/0.1.3/ \ | ||
| && wget https://github.com/ksahlin/namfinder/archive/refs/tags/v0.1.3.tar.gz -O /opt2/namfinder/0.1.3/v0.1.3.tar.gz \ | ||
| && tar -zvxf /opt2/namfinder/0.1.3/v0.1.3.tar.gz -C /opt2/namfinder/0.1.3/ \ | ||
| && rm -f /opt2/namfinder/0.1.3/v0.1.3.tar.gz \ | ||
| && cd /opt2/namfinder/0.1.3/namfinder-0.1.3/ \ | ||
| # Build to be compatiable with most | ||
| # Intel x86 CPUs, should work with | ||
| # old hardware, i.e. sandybridge | ||
| && cmake -B build -DCMAKE_C_FLAGS="-msse4.2" -DCMAKE_CXX_FLAGS="-msse4.2" \ | ||
| && make -j -C build | ||
|
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||
| ENV PATH="${PATH}:/opt2/namfinder/0.1.3/namfinder-0.1.3/build" | ||
| WORKDIR /opt2 | ||
|
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||
| ############### INSTALL ################ | ||
| # Install any bioinformatics packages | ||
| # available with pypi or CRAN/BioC | ||
| RUN ln -sf /usr/bin/python3 /usr/bin/python | ||
| RUN pip3 install --upgrade pip \ | ||
| && pip3 install Cython \ | ||
| && pip3 install bcbio-gff \ | ||
| && pip3 install biopython \ | ||
| && pip3 install bx-python \ | ||
| && pip3 install matplotlib \ | ||
| && pip3 install numpy \ | ||
| && pip3 install pandas \ | ||
| && pip3 install psutil \ | ||
| && pip3 install pybedtools \ | ||
| && pip3 install pysam \ | ||
| && pip3 install scipy \ | ||
| && pip3 install ultra-bioinformatics | ||
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||
| # !TODO: Install cDNA_Cupcake from Github | ||
| # And install R packages, and finally | ||
| # install SQANTI3/v5.1.2 | ||
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| ################ POST ################# | ||
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