Mercurial > repos > morinlab > ensembl_vep
changeset 9:3da95f8a328a draft
Uploaded
| author | morinlab |
|---|---|
| date | Fri, 27 Jan 2017 17:05:55 -0500 |
| parents | e9d366311add |
| children | 651731609448 |
| files | download_genome.xml |
| diffstat | 1 files changed, 12 insertions(+), 1 deletions(-) [+] |
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--- a/download_genome.xml Fri Jan 27 16:49:39 2017 -0500 +++ b/download_genome.xml Fri Jan 27 17:05:55 2017 -0500 @@ -6,6 +6,7 @@ <requirement type="package" version="84">ensembl_vep</requirement> </requirements> <command> + #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) @@ -14,7 +15,16 @@ --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 + ; 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; @@ -22,6 +32,7 @@ </command> <inputs> <expand macro="genome_list" /> + </inputs> <outputs> <data format="txt" name="output"/>