Mercurial > repos > morinlab > ensembl_vep
changeset 20:9c48b6d4b110 draft default tip
Deleted selected files
| author | morinlab |
|---|---|
| date | Fri, 27 Jan 2017 17:37:36 -0500 |
| parents | 56d99be4cc8f |
| children | |
| files | download_genome.xml |
| diffstat | 1 files changed, 0 insertions(+), 48 deletions(-) [+] |
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--- a/download_genome.xml Fri Jan 27 17:36:09 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<tool id="download_genome" name="Get Genome" version="1.0.0"> - <description> - Download and Index Genomes and Reference files used by Ensemble VEP - </description> - <requirements> - <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) - --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; - </command> - <inputs> - <expand macro="genome_list" /> - <param name="use_mirror" type="boolean" checked="false" label="use North American mirror site for download" display="radio" truevalue="yes" falsevalue="no"/> - </inputs> - <outputs> - <data format="txt" name="output"/> - </outputs> - <stdio> - <exit_code range="1:" level="fatal" description="Failure" /> - </stdio> - <macros> - <import>ensembl_vep_macros.xml</import> - </macros> - -</tool>