updated tool download scripts

imgag · Sep 9, 2024 · 0d724e2 · 0d724e2
1 parent d735ef8
commit 0d724e2
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Showing 9 changed files with 2 additions and 3 deletions.
diff --git a/data/download_GRCh37.sh b/data/download_GRCh37.sh
diff --git a/data/download_GRCh38.sh b/data/download_GRCh38.sh
diff --git a/data/download_GRCh38_alt.sh b/data/download_GRCh38_alt.sh
diff --git a/data/download_hg38.sh b/data/download_hg38.sh
diff --git 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
@@ -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
diff --git a/data/download_tools_somatic.sh b/data/download_tools_somatic.sh
diff --git a/data/download_tools_vep.sh b/data/download_tools_vep.sh