| Previous changeset 8:c762a1cd357e (2022-01-27) Next changeset 10:74db03ff999e (2022-04-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468" |
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modified:
README.md interproscan.xml macros.xml |
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| diff -r c762a1cd357e -r c55643c3d813 README.md --- a/README.md Thu Jan 27 09:46:37 2022 +0000 +++ b/README.md Fri Feb 11 17:20:19 2022 +0000 |
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| @@ -10,3 +10,71 @@ - SMART data (THRESHOLD file) As a Galaxy instance admin, you can install those manually if needed, as long as you (and the Galaxy users) respect the respective licenses. + +## Installing licensed components manually + +All the following steps assume that: + +- You agree with each software license +- InterProScan was installed using Conda in the `IPRSCAN_DIR` directory +- You have run the InterProScan data manager which placed the data files in the `IPRSCAN_DATA_DIR` directory (e.g. `/data/db/data_managers/interproscan/5.54-87.0/`) + +Everytime you upgrade InterProScan, you'll need to do the same things: modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file + add the SMART file. + +### SignalP + +Download and install SignalP 4.1 from https://services.healthtech.dtu.dk/service.php?SignalP-4.1 + +Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your SignalP install (ie the downloaded archive unzipped in `/path/to/signalp/4.1/`): + +``` +binary.signalp.path=/path/to/signalp/4.1/signalp +signalp.perl.library.dir=/path/to/signalp/4.1/lib/ +``` + +Make sure the SignalP script begins like this: + +``` +#!/usr/bin/env perl +``` + +And make sure, you have properly set `$ENV{SIGNALP}` in the SignalP script (around line 13). + +### TMHMM + +Download and install TMHMM 2.0c from https://services.healthtech.dtu.dk/service.php?TMHMM-2.0 + +Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your TMHMM install (ie the downloaded archive unzipped in `/path/to/tmhmm/2.0c/`): + +``` +binary.tmhmm.path=/path/to/tmhmm/2.0c/bin/decodeanhmm.Linux_x86_64 +tmhmm.model.path=/path/to/tmhmm/2.0c/lib/TMHMM2.0.model +``` + +### Phobius + +Download Phobius from https://phobius.sbc.su.se/data.html + +Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your Phobius install (ie the downloaded archive unzipped in `/pth/to/phobiu/`): + +``` +binary.phobius.pl.path=/path/to/phobius/phobius.pl +``` + +Make sure the phobius.pl script begins like this: + +``` +#!/usr/bin/env perl +``` + +### SMART data + +Download SMART data from https://software.embl-em.de/software/18 (choose SMART 7.1) + +Copy the THRESHOLDS file from the archive into `${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS` + +Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use this SMART file: + +``` +smart.threshold.path=${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS +``` |
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| diff -r c762a1cd357e -r c55643c3d813 interproscan.xml --- a/interproscan.xml Thu Jan 27 09:46:37 2022 +0000 +++ b/interproscan.xml Fri Feb 11 17:20:19 2022 +0000 |
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| @@ -16,6 +16,9 @@ && sed 's|^\(data.directory=\).*$|\1${database.fields.path}/data|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties && +## Java doesn't read the HOME env var +export _JAVA_OPTIONS=-Duser.home=\$HOME +&& ## Now run interproscan interproscan.sh @@ -31,7 +34,7 @@ #else: --applications ${','.join($applications)} #end if ---tempdir \$TEMP +--tempdir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} $pathways $goterms |
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| diff -r c762a1cd357e -r c55643c3d813 macros.xml --- a/macros.xml Thu Jan 27 09:46:37 2022 +0000 +++ b/macros.xml Fri Feb 11 17:20:19 2022 +0000 |
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| @@ -6,7 +6,7 @@ The version should also be bumped in test-data/interproscan.loc --> <token name="@TOOL_VERSION@">5.54-87.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="citations"> <citations> |