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Upgrade enaBrowserTools to v1.6 #88

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Upgrade enaBrowserTools to v1.6 #88

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4 changes: 2 additions & 2 deletions scripts/install_dependencies.sh
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Expand Up @@ -69,8 +69,8 @@ cp -s bwa-0.7.15/bwa .

#_____________________ enaBrowserTools ____________________#
cd $install_root
wget -q https://github.com/enasequence/enaBrowserTools/archive/v1.5.4.tar.gz
tar xf v1.5.4.tar.gz
wget -q https://github.com/enasequence/enaBrowserTools/archive/v1.6.tar.gz
tar xf v1.6.tar.gz


#_________________________ FASTQC ________________________#
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4 changes: 2 additions & 2 deletions singularity/clockwork_container.def
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Expand Up @@ -5,15 +5,15 @@ MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%environment
PERL5LIB=/bioinf-tools/vcftools-0.1.15/install/share/perl/5.24.1/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$PERL5LIB
export PERL5LIB
PATH=/bioinf-tools/:/bioinf-tools/cortex/bin/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.5.4/python3:/clockwork/scripts/:$PATH
PATH=/bioinf-tools/:/bioinf-tools/cortex/bin/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.6/python3:/clockwork/scripts/:$PATH

%setup
mkdir $SINGULARITY_ROOTFS/clockwork
rsync -a ../python ../nextflow ../scripts $SINGULARITY_ROOTFS/clockwork/

%post
#_____________________ setup $PATH _______________________#
export PATH=/bioinf-tools/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.5.4/python3:/clockwork/scripts/:$PATH
export PATH=/bioinf-tools/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.6/python3:/clockwork/scripts/:$PATH
export PERL5LIB=/bioinf-tools/vcftools-0.1.15/install/share/perl/5.24.1/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$PERL5LIB
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

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2 changes: 1 addition & 1 deletion vagrant/Vagrantfile
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Expand Up @@ -52,7 +52,7 @@ Vagrant.configure(2) do |config|

# Set up env vars
config.vm.provision "shell", privileged: false, inline: <<-SHELL
echo "export PATH=/bioinf-tools/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.5.4/python3:$PATH" >> $HOME/.bashrc
echo "export PATH=/bioinf-tools/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.6/python3:$PATH" >> $HOME/.bashrc
echo "export PERL5LIB=/bioinf-tools/vcftools-0.1.15/install/share/perl/5.24.1/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$PERL5LIB" >> $HOME/.bashrc
echo "export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH" >> $HOME/.bashrc
SHELL
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