Mercurial > repos > morinlab > ensembl_vep
changeset 19:56d99be4cc8f draft
Uploaded
| author | morinlab |
|---|---|
| date | Fri, 27 Jan 2017 17:36:09 -0500 |
| parents | 191b0dfe8237 |
| children | 9c48b6d4b110 |
| files | download_cache.xml |
| diffstat | 1 files changed, 48 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<tool id="download_cache" name="Get VEP Cache" 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>