From 0d724e29dfe91b90b2fca5e456447225db09824e Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Mon, 9 Sep 2024 15:19:03 +0200 Subject: [PATCH] updated tool download scripts --- data/download_GRCh37.sh | 0 data/download_GRCh38.sh | 0 data/download_GRCh38_alt.sh | 0 data/download_hg38.sh | 0 data/download_tools.sh | 4 ++-- data/download_tools_longread.sh | 1 - data/download_tools_rna.sh | 0 data/download_tools_somatic.sh | 0 data/download_tools_vep.sh | 0 9 files changed, 2 insertions(+), 3 deletions(-) mode change 100644 => 100755 data/download_GRCh37.sh mode change 100644 => 100755 data/download_GRCh38.sh mode change 100644 => 100755 data/download_GRCh38_alt.sh mode change 100644 => 100755 data/download_hg38.sh mode change 100644 => 100755 data/download_tools.sh mode change 100644 => 100755 data/download_tools_longread.sh mode change 100644 => 100755 data/download_tools_rna.sh mode change 100644 => 100755 data/download_tools_somatic.sh mode change 100644 => 100755 data/download_tools_vep.sh diff --git a/data/download_GRCh37.sh b/data/download_GRCh37.sh old mode 100644 new mode 100755 diff --git a/data/download_GRCh38.sh b/data/download_GRCh38.sh old mode 100644 new mode 100755 diff --git a/data/download_GRCh38_alt.sh b/data/download_GRCh38_alt.sh old mode 100644 new mode 100755 diff --git a/data/download_hg38.sh b/data/download_hg38.sh old mode 100644 new mode 100755 diff --git a/data/download_tools.sh b/data/download_tools.sh old mode 100644 new mode 100755 index b6cd1b7af..826a9c278 --- a/data/download_tools.sh +++ b/data/download_tools.sh @@ -115,7 +115,6 @@ git checkout v1.0.3 && git submodule update --recursive --init mkdir -p build && cd build cmake .. cmake --build . -cmake --install . #download and build samblaster cd $folder @@ -165,7 +164,7 @@ rm interop-1.2.4-Linux-GNU.tar.gz #download Circos cd $folder -wget http://circos.ca/distribution/circos-0.69-9.tgz +wget --no-check-certificate https://circos.ca/distribution/circos-0.69-9.tgz tar xzf circos-0.69-9.tgz rm circos-0.69-9.tgz # install required Perl modules for Circos in a subfolder @@ -210,6 +209,7 @@ chmod 755 bedtools.static cd $folder wget https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip unzip gatk-4.6.0.0.zip +rm -rf gatk-4.6.0.0.zip #download illuminia ORA decompression tool cd $folder diff --git a/data/download_tools_longread.sh b/data/download_tools_longread.sh old mode 100644 new mode 100755 index 870947e7c..1d0d48048 --- a/data/download_tools_longread.sh +++ b/data/download_tools_longread.sh @@ -82,7 +82,6 @@ cd .. cd $folder wget https://github.com/bcgsc/straglr/releases/download/v1.5.1/straglr-1.5.1.tar.gz tar xzf straglr-1.5.1.tar.gz -mv straglr straglr-1.5.1 rm straglr-1.5.1.tar.gz #download StraglrOn diff --git a/data/download_tools_rna.sh b/data/download_tools_rna.sh old mode 100644 new mode 100755 diff --git a/data/download_tools_somatic.sh b/data/download_tools_somatic.sh old mode 100644 new mode 100755 diff --git a/data/download_tools_vep.sh b/data/download_tools_vep.sh old mode 100644 new mode 100755