# HG changeset patch # User morinlab # Date 1485556569 18000 # Node ID 56d99be4cc8f126e767438830eb918b42c0641c2 # Parent 191b0dfe82378c83856af13aee9c696a1c8e30e7 Uploaded diff -r 191b0dfe8237 -r 56d99be4cc8f download_cache.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/download_cache.xml Fri Jan 27 17:36:09 2017 -0500 @@ -0,0 +1,48 @@ + + + Download and Index Genomes and Reference files used by Ensemble VEP + + + ensembl_vep + + + #if $use_mirror.value == "no": + perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl + --AUTO cf + --SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1) + --CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache + #if "-" in $species_select.value + --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2) + #end if + ; + #else: + perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl + --AUTO cf + --SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1) + --CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache + --CACHEURL ftp://ftp03.bcgsc.ca/public/ensembl/VEP/ --FASTAURL ftp://ftp03.bcgsc.ca/public/ensembl/ + #if "-" in $species_select.value + --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2) + #end if + ; + #end if + gzip -d \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa.gz; + samtools faidx \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa; + + env > $output; + + + + + + + + + + + + + ensembl_vep_macros.xml + + +