diff --git a/scripts/install_dependencies.sh b/scripts/install_dependencies.sh index 3906f24..d2420d1 100755 --- a/scripts/install_dependencies.sh +++ b/scripts/install_dependencies.sh @@ -69,8 +69,8 @@ cp -s bwa-0.7.15/bwa . #_____________________ enaBrowserTools ____________________# cd $install_root -wget -q https://github.com/enasequence/enaBrowserTools/archive/v1.5.4.tar.gz -tar xf v1.5.4.tar.gz +wget -q https://github.com/enasequence/enaBrowserTools/archive/v1.6.tar.gz +tar xf v1.6.tar.gz #_________________________ FASTQC ________________________# diff --git a/singularity/clockwork_container.def b/singularity/clockwork_container.def index a31b226..446eaad 100644 --- a/singularity/clockwork_container.def +++ b/singularity/clockwork_container.def @@ -5,7 +5,7 @@ MirrorURL: http://us.archive.ubuntu.com/ubuntu/ %environment PERL5LIB=/bioinf-tools/vcftools-0.1.15/install/share/perl/5.24.1/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$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 @@ -13,7 +13,7 @@ PATH=/bioinf-tools/:/bioinf-tools/cortex/bin/:/bioinf-tools/cortex/scripts/analy %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:$LD_LIBRARY_PATH diff --git a/vagrant/Vagrantfile b/vagrant/Vagrantfile index c5481c2..f489282 100644 --- a/vagrant/Vagrantfile +++ b/vagrant/Vagrantfile @@ -52,7 +52,7 @@ Vagrant.configure(2) do |config| # Set up env vars config.vm.provision "shell", privileged: false, inline: <<-SHELL - echo "export PATH=/bioinf-tools/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.5.4/python3:$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