Commit b6b1b78a authored by Blaise Li's avatar Blaise Li
Browse files

Recording tools versions in /usr/share/doc.

parent 74013222
...@@ -13,16 +13,14 @@ From:workflows_base.sif ...@@ -13,16 +13,14 @@ From:workflows_base.sif
#git clone --recurse-submodules https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git #git clone --recurse-submodules https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git
git clone https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git git clone https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git
cd bioinfo_utils cd bioinfo_utils
WORKFLOWS_VERSION=$(git log | head -1 | cut -d " " -f2)
pip install -r requirements.txt pip install -r requirements.txt
# Recording program versions prog="Python packages"
for prog in bedops bedtools bowtie2 cutadapt hisat2 parallel samtools
do
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog} --version" >> /usr/local/share/doc/program_versions.txt pip freeze >> /usr/local/share/doc/program_versions.txt
done prog="Workflows"
prog="featureCounts"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog} -v" 2>> /usr/local/share/doc/program_versions.txt echo "${WORKFLOWS_VERSION}" >> /usr/local/share/doc/program_versions.txt
%environment %environment
export LC_ALL=C export LC_ALL=C
......
...@@ -16,6 +16,7 @@ Stage: build-haskell ...@@ -16,6 +16,7 @@ Stage: build-haskell
cd /usr/local/src cd /usr/local/src
git clone https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git git clone https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git
cd bioinfo_utils cd bioinfo_utils
HASKELL_TOOLS_VERSION=$(git log | head -1 | cut -d " " -f2)
git submodule update --init --remote --merge git submodule update --init --remote --merge
# Note that currently only remove-duplicates-from-sorted-fastq # Note that currently only remove-duplicates-from-sorted-fastq
# and trim-t-tail-from-fastq are copied to the next stage # and trim-t-tail-from-fastq are copied to the next stage
...@@ -24,6 +25,8 @@ Stage: build-haskell ...@@ -24,6 +25,8 @@ Stage: build-haskell
do do
(cd ${dir} && grep "local" install.sh && ./install.sh) (cd ${dir} && grep "local" install.sh && ./install.sh)
done done
echo "# Haskell tools" >> /usr/local/share/doc/program_versions.txt
echo "${HASKELL_TOOLS_VERSION}" >> /usr/local/share/doc/program_versions.txt
Bootstrap:docker Bootstrap:docker
From:python:3.7-buster From:python:3.7-buster
...@@ -31,6 +34,7 @@ From:python:3.7-buster ...@@ -31,6 +34,7 @@ From:python:3.7-buster
%files from build-haskell %files from build-haskell
/usr/local/bin/remove-duplicates-from-sorted-fastq /usr/local/bin/remove-duplicates-from-sorted-fastq
/usr/local/bin/trim-t-tail-from-fastq /usr/local/bin/trim-t-tail-from-fastq
/usr/local/share/doc/program_versions.txt
%post %post
apt-get -y update apt-get -y update
...@@ -41,6 +45,16 @@ From:python:3.7-buster ...@@ -41,6 +45,16 @@ From:python:3.7-buster
# run_pipeline.sh (and maybe other tools) needs bc # run_pipeline.sh (and maybe other tools) needs bc
apt-get -y install bc rsync apt-get -y install bc rsync
apt-get -y install bedops bedtools bowtie2 cutadapt subread hisat2 parallel samtools apt-get -y install bedops bedtools bowtie2 cutadapt subread hisat2 parallel samtools
# Recording program versions
for prog in bedops bedtools bowtie2 cutadapt hisat2 parallel samtools
do
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog} --version" >> /usr/local/share/doc/program_versions.txt
done
# subread provides featureCounts
prog="featureCounts"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog} -v" 2>> /usr/local/share/doc/program_versions.txt
# Some programs are not provided by debian # Some programs are not provided by debian
# mkdir -p /usr/local/src # mkdir -p /usr/local/src
##################### #####################
...@@ -49,9 +63,13 @@ From:python:3.7-buster ...@@ -49,9 +63,13 @@ From:python:3.7-buster
cd /usr/local/src cd /usr/local/src
git clone https://github.com/lh3/bioawk.git git clone https://github.com/lh3/bioawk.git
cd bioawk cd bioawk
BIOAWK_VERSION=$(git log | head -1 | cut -d " " -f2)
apt install -y byacc apt install -y byacc
make make
ln -s /usr/local/src/bioawk/bioawk /usr/local/bin/. ln -s /usr/local/src/bioawk/bioawk /usr/local/bin/.
prog="bioawk"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
echo "${BIOAWK_VERSION}" >> /usr/local/share/doc/program_versions.txt
########################## ##########################
# Installing fastq-tools # # Installing fastq-tools #
########################## ##########################
...@@ -62,6 +80,10 @@ From:python:3.7-buster ...@@ -62,6 +80,10 @@ From:python:3.7-buster
./configure ./configure
make make
make install make install
# fastq-tools provides fastq-sort
prog="fastq-sort"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog} --version" >> /usr/local/share/doc/program_versions.txt
######################### #########################
# Installing kent utils # # Installing kent utils #
######################### #########################
...@@ -69,15 +91,24 @@ From:python:3.7-buster ...@@ -69,15 +91,24 @@ From:python:3.7-buster
#mkdir UCSC-tools #mkdir UCSC-tools
#cd UCSC-tools #cd UCSC-tools
rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/. rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/.
prog="bedGraphToBigWig"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog}" 2>> /usr/local/share/doc/program_versions.txt
# It is possible to test whether the R install is already OK # It is possible to test whether the R install is already OK
deb_source="deb http://cran.irsn.fr/bin/linux/debian buster-cran35/" deb_source="deb http://cran.irsn.fr/bin/linux/debian buster-cran35/"
echo ${deb_source} >> /etc/apt/sources.list.d/cran.list echo ${deb_source} >> /etc/apt/sources.list.d/cran.list
apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF' apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
apt-get -y update apt-get -y update
apt-get -y install r-base-core r-base-dev apt-get -y install r-base-core r-base-dev
prog="R"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
eval "${prog} --version" >> /usr/local/share/doc/program_versions.txt
R -e 'install.packages("BiocManager")' R -e 'install.packages("BiocManager")'
R -e 'BiocManager::install(ask=FALSE)' R -e 'BiocManager::install(ask=FALSE)'
R -e 'BiocManager::install(c("docopt", "DESeq2"), ask=FALSE)' R -e 'BiocManager::install(c("docopt", "DESeq2"), ask=FALSE)'
prog="DESeq2"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
R -q -e 'packageVersion("DESeq2")' >> /usr/local/share/doc/program_versions.txt
# To use the "local" python, not the system one. # To use the "local" python, not the system one.
export PATH="/usr/local/bin":$PATH export PATH="/usr/local/bin":$PATH
......
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