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Commit 9e10aafe authored by Alexis Mergez's avatar Alexis Mergez
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v1.0f

Patched the definition file even more
parent 426a572e
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Pipeline #161538 passed with stages
in 21 minutes and 13 seconds
......@@ -57,7 +57,8 @@ Stage: build
cmake \
libjemalloc-dev \
python3-distutils \
time
time \
libncurses5-dev
apt-get clean
apt-get purge
rm -rf /var/lib/apt/lists/*
......@@ -105,14 +106,14 @@ Stage: build
ls -lRa /apps/cactus/bin
cd /apps
# Installing pggb
cd /apps
wget https://github.com/pangenome/pggb/archive/refs/tags/v0.5.4.tar.gz
tar -zxvf v0.5.4.tar.gz
cd pggb-0.5.4
# Installing wfmash
cd /apps
wget https://github.com/waveygang/wfmash/releases/download/v0.10.5/wfmash-v0.10.5.tar.gz
tar -zxvf wfmash-v0.10.5.tar.gz
mv wfmash-v0.10.5 wfmash
......@@ -129,7 +130,6 @@ Stage: build
rm -rf wfmash
# Installing seqwish
cd /apps
git clone --recursive https://github.com/ekg/seqwish \
&& cd seqwish \
&& git pull \
......@@ -141,7 +141,6 @@ Stage: build
&& rm -rf seqwish
# Installing smoothgx
cd /apps
git clone --recursive https://github.com/pangenome/smoothxg \
&& cd smoothxg \
&& git pull \
......@@ -162,7 +161,6 @@ Stage: build
cargo --help
# Installing GFAffix
cd /apps
git clone https://github.com/marschall-lab/GFAffix.git \
&& cd GFAffix \
&& git pull \
......@@ -176,11 +174,9 @@ Stage: build
pip install multiqc==1.18
# Installing VG
cd /apps
wget https://github.com/vgteam/vg/releases/download/v1.53.0/vg && chmod +x vg && mv vg /apps/bin/vg
# Installing vcfbub
cd /apps
git clone https://github.com/pangenome/vcfbub \
&& cd vcfbub \
&& git pull \
......@@ -191,7 +187,6 @@ Stage: build
&& rm -rf vcfbub
# Installing vcflib
cd /apps
git clone --recursive https://github.com/vcflib/vcflib.git \
&& cd vcflib \
&& git checkout 7c1a31a430d339adcb9a0c2fd3fd02d3b30e3549 \
......@@ -208,7 +203,6 @@ Stage: build
pip install pycairo==1.23.0
# Installing additionnal tools
cd /apps
git clone https://github.com/ekg/fastix.git \
&& cd fastix \
&& git pull \
......@@ -218,7 +212,6 @@ Stage: build
&& cd ../ \
&& rm -rf fastix
cd /apps
git clone https://github.com/ekg/pafplot.git \
&& cd pafplot \
&& git pull \
......@@ -236,18 +229,15 @@ Stage: build
chmod a+rx /apps/bin/partition-before-pggb
# Mummer adjustments
cd /apps
wget https://github.com/mummer4/mummer/releases/download/v4.0.0rc1/mummer-4.0.0rc1.tar.gz \
&& tar -xf mummer-4.0.0rc1.tar.gz && cd mummer-4.0.0rc1 && ./configure && make && make install && cd ../
ldconfig
cd /apps
wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.12.1/rtg-tools-3.12.1-linux-x64.zip \
&& unzip rtg-tools-3.12.1-linux-x64.zip && sed -i 's/read -r -p "Would you like to enable automatic usage logging (y\/n)? " REPLY/REPLY="n"/g' /rtg-tools-3.12.1/rtg \
&& ln -s /rtg-tools-3.12.1/rtg /apps/bin/ && rtg help
# Installing base R
cd /apps
apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-key B8F25A8A73EACF41 \
&& echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" > /etc/apt/sources.list.d/r-packages.list \
&& apt update \
......@@ -259,7 +249,6 @@ Stage: build
&& R CMD INSTALL data.table_1.14.8.tar.gz
# Installing Bedtools
cd /apps
wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static \
&& mv bedtools.static /apps/bin/bedtools \
&& chmod +x /apps/bin/bedtools
......@@ -272,7 +261,7 @@ Stage: build
wget https://github.com/samtools/htslib/releases/download/1.19/htslib-1.19.tar.bz2
tar -xvf htslib-1.19.tar.bz2
cd htslib-1.19
./configure --prefix=/usr/local
./configure --prefix=/apps
make -j $(nproc)
make install
......@@ -281,7 +270,7 @@ Stage: build
wget https://github.com/samtools/samtools/releases/download/1.19/samtools-1.19.tar.bz2
tar -xvf samtools-1.19.tar.bz2
cd samtools-1.19
./configure --prefix=/usr/local
./configure --prefix=/apps
make -j $(nproc)
make install
......
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