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p3-runtime-bootstrap-2345.def
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p3-runtime-bootstrap-2345.def
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Bootstrap: localimage
From: /disks/disk0/olson/images/p3-centos6-runtime-2020-0520.step2.sif
#From: images/p3-runtime-bootstrap-1.sif
#From: images/bs1-with-openssl.sif
#From: images/base-centos6-2019-1127.sif
From: /disks/disk0/olson/images/p3-centos6-2020-0520.sif
#From: /disks/olson/images/p3-centos6-2020-0210.sif
#From: images/base-os.sif
%files
cpan-packages.tar.gz /
%post
yum install -y cmake java-1.8.0-openjdk-devel
BASE=/opt/patric-common
RT=$BASE/runtime
mkdir -p $RT
git clone https://github.com/olsonanl/bootstrap
cd bootstrap
cd kb_perl_runtime
rm -rf cpan-packages
tar xzfp /cpan-packages.tar.gz
cd ..
./bootstrap_modules.pl -d $RT -m modules-patric3-core.dat
./bootstrap_modules.pl -d $RT -m modules-patric3-build-tools.dat
./bootstrap_modules.pl -d $RT -m modules-patric3-anno-core.dat
./bootstrap_modules.pl -d $RT -m modules-patric3-bio-core.dat
export BUILD_TOOLS=$RT/build-tools
./bootstrap_modules.pl -d $RT -m modules-patric3-ngs-core.dat
mkdir -p $BASE/app-runtime/variation
./bootstrap_modules.pl -d $BASE/app-runtime/variation -m modules-app-variation.dat
cd /bootstrap/kb_prok_tuxedo
./install_prok_tuxedo.sh /opt/patric-common/runtime
cd /bootstrap
git clone --recursive https://github.com/PATRIC3/freebayes.git
cd freebayes
make
cp bin/freebayes bin/bamleftalign /opt/patric-common/app-runtime/variation/bin/
cp scripts/freebayes-parallel /opt/patric-common/app-runtime/variation/bin/freebayes-parallel
chmod +x /opt/patric-common/app-runtime/variation/bin/freebayes-parallel
# part of modules-patric3-ngs-core
cd /bootstrap/p3_bedtools
tar=`cat TARFILE`
file=`basename $tar`
curl -O -L $tar
tar xzfp $file
cd bedtools2
make -j8 prefix=/opt/patric-common/runtime
make prefix=/opt/patric-common/runtime install
## cd /bootstrap/p3_samstat
## (export PATH=$PATH:/opt/patric-common/runtime/samtools-1.9/bin; \
## ./build.package /opt/patric-common/runtime)
cd /bootstrap
curl -O -L http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.0.tar.gz
tar xzfp stringtie-1.3.0.tar.gz
cd stringtie-1.3.0
make release
cp stringtie /opt/patric-common/runtime/bin
cd ..
curl -O -L https://github.com/infphilo/hisat2/archive/0f01dc6397a.tar.gz
tar xzfp 0f01dc6397a.tar.gz
cd hisat2-0f01dc6397a/
make -j6
cp hisat2 hisat2-* /opt/patric-common/runtime/bin
cd /tmp
rm -rf FastQC fastqc*
curl -O -L https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip
unzip fastqc_v0.11.7.zip
cp -r FastQC /opt/patric-common/runtime/FastQC-0.11.7
cd /opt/patric-common/runtime/bin
ln -s ../FastQC-0.11.7/fastqc .
chmod +x fastqc
#
# Expression transform fails under modern pandas
#
/opt/patric-common/runtime/bin/pip2 install --upgrade pandas==0.16