view download_genome.xml @ 11:a7f44ff74b74 draft

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<tool id="download_genome" name="Get Genome" version="1.0.0">
    <description>
      Download and Index Genomes using 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" />
      
    </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>