diff README.md @ 9:c55643c3d813 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"

--- a/README.md	Thu Jan 27 09:46:37 2022 +0000
+++ b/README.md	Fri Feb 11 17:20:19 2022 +0000
@@ -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
+```