Mercurial > repos > morinlab > ensembl_vep
changeset 11:a7f44ff74b74 draft
Uploaded
| author | morinlab |
|---|---|
| date | Fri, 27 Jan 2017 17:09:29 -0500 |
| parents | 651731609448 |
| children | f50de21e9cd0 |
| files | download_genome.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/download_genome.xml Fri Jan 27 17:06:10 2017 -0500 +++ b/download_genome.xml Fri Jan 27 17:09:29 2017 -0500 @@ -21,10 +21,11 @@ --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 - ; + #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;