--- 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
+```

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

--- a/macros.xml	Thu Jan 27 09:46:37 2022 +0000
+++ b/macros.xml	Fri Feb 11 17:20:19 2022 +0000
@@ -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>