Mercurial > repos > bgruening > interproscan

comparison interproscan.xml @ 9:c55643c3d813 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
author iuc
date Fri, 11 Feb 2022 17:20:19 +0000
parents 1207025b9b9c
children 98cafcbd2578
comparison
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8:c762a1cd357e 9:c55643c3d813
14 ## Adapt properties file to use data from data table 14 ## Adapt properties file to use data from data table
15 mkdir -p \$HOME/.interproscan-5 15 mkdir -p \$HOME/.interproscan-5
16 && 16 &&
17 sed 's|^\(data.directory=\).*$|\1${database.fields.path}/data|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties 17 sed 's|^\(data.directory=\).*$|\1${database.fields.path}/data|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties
18 && 18 &&
19 ## Java doesn't read the HOME env var
20 export _JAVA_OPTIONS=-Duser.home=\$HOME
21 &&
19 22
20 ## Now run interproscan 23 ## Now run interproscan
21 interproscan.sh 24 interproscan.sh
22 25
23 ## disables the precalculated lookup service, all calculation will be run locally 26 ## disables the precalculated lookup service, all calculation will be run locally
29 #if $licensed.use == 'true' and $licensed.applications_licensed: 32 #if $licensed.use == 'true' and $licensed.applications_licensed:
30 --applications ${','.join($applications)},${','.join($licensed.applications_licensed)} 33 --applications ${','.join($applications)},${','.join($licensed.applications_licensed)}
31 #else: 34 #else:
32 --applications ${','.join($applications)} 35 --applications ${','.join($applications)}
33 #end if 36 #end if
34 --tempdir \$TEMP 37 --tempdir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
35 38
36 $pathways 39 $pathways
37 $goterms 40 $goterms
38 $iprlookup 41 $iprlookup
39 42