Mercurial > repos > bgruening > interproscan

comparison README.md @ 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 fcedfe919603
children 74db03ff999e
comparison
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8:c762a1cd357e 9:c55643c3d813
8 - TMHMM 8 - TMHMM
9 - Phobius 9 - Phobius
10 - SMART data (THRESHOLD file) 10 - SMART data (THRESHOLD file)
11 11
12 As a Galaxy instance admin, you can install those manually if needed, as long as you (and the Galaxy users) respect the respective licenses. 12 As a Galaxy instance admin, you can install those manually if needed, as long as you (and the Galaxy users) respect the respective licenses.
13
14 ## Installing licensed components manually
15
16 All the following steps assume that:
17
18 - You agree with each software license
19 - InterProScan was installed using Conda in the `IPRSCAN_DIR` directory
20 - 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/`)
21
22 Everytime you upgrade InterProScan, you'll need to do the same things: modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file + add the SMART file.
23
24 ### SignalP
25
26 Download and install SignalP 4.1 from https://services.healthtech.dtu.dk/service.php?SignalP-4.1
27
28 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your SignalP install (ie the downloaded archive unzipped in `/path/to/signalp/4.1/`):
29
30 ```
31 binary.signalp.path=/path/to/signalp/4.1/signalp
32 signalp.perl.library.dir=/path/to/signalp/4.1/lib/
33 ```
34
35 Make sure the SignalP script begins like this:
36
37 ```
38 #!/usr/bin/env perl
39 ```
40
41 And make sure, you have properly set `$ENV{SIGNALP}` in the SignalP script (around line 13).
42
43 ### TMHMM
44
45 Download and install TMHMM 2.0c from https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
46
47 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your TMHMM install (ie the downloaded archive unzipped in `/path/to/tmhmm/2.0c/`):
48
49 ```
50 binary.tmhmm.path=/path/to/tmhmm/2.0c/bin/decodeanhmm.Linux_x86_64
51 tmhmm.model.path=/path/to/tmhmm/2.0c/lib/TMHMM2.0.model
52 ```
53
54 ### Phobius
55
56 Download Phobius from https://phobius.sbc.su.se/data.html
57
58 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your Phobius install (ie the downloaded archive unzipped in `/pth/to/phobiu/`):
59
60 ```
61 binary.phobius.pl.path=/path/to/phobius/phobius.pl
62 ```
63
64 Make sure the phobius.pl script begins like this:
65
66 ```
67 #!/usr/bin/env perl
68 ```
69
70 ### SMART data
71
72 Download SMART data from https://software.embl-em.de/software/18 (choose SMART 7.1)
73
74 Copy the THRESHOLDS file from the archive into `${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS`
75
76 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use this SMART file:
77
78 ```
79 smart.threshold.path=${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS
80 ```