Mercurial > repos > bgruening > interproscan
comparison interproscan.xml @ 9:c55643c3d813 draft
"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
equal
deleted
inserted
replaced
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 |