annotate README.md @ 11:98cafcbd2578 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit c8c7a5c3fa0560d6bc6bbb45cfbff12621ab2f43"
author iuc
date Fri, 29 Apr 2022 20:14:21 +0000
parents 74db03ff999e
children 74810db257cc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
1 # InterProScan
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
2
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
3 ## Licensed software/data
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
5 The standard install of InterProScan does not include the following components, because their license does not allow redistribution:
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
6
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
7 - SignalP
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
8 - TMHMM
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
9 - Phobius
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
10 - SMART data (THRESHOLD file)
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
11
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
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.
9
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
13
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
14 ## Installing licensed components manually
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
15
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
16 All the following steps assume that:
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
17
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
18 - You agree with each software license
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
19 - InterProScan was installed using Conda in the `IPRSCAN_DIR` directory
10
74db03ff999e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit a3d8961c9561d96f099e4eb4ffc5a64b26791af6"
iuc
parents: 9
diff changeset
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/5.55-88.0/`)
9
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
21
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
22 Everytime you upgrade InterProScan, you'll need to do the same things: modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file + add the SMART file.
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
23
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
24 ### SignalP
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
25
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
26 Download and install SignalP 4.1 from https://services.healthtech.dtu.dk/service.php?SignalP-4.1
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
27
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
28 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your SignalP install (ie the downloaded archive unzipped in `/path/to/signalp/4.1/`):
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
29
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
30 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
31 binary.signalp.path=/path/to/signalp/4.1/signalp
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
32 signalp.perl.library.dir=/path/to/signalp/4.1/lib/
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
33 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
34
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
35 Make sure the SignalP script begins like this:
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
36
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
37 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
38 #!/usr/bin/env perl
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
39 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
40
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
41 And make sure, you have properly set `$ENV{SIGNALP}` in the SignalP script (around line 13).
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
42
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
43 ### TMHMM
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
44
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
45 Download and install TMHMM 2.0c from https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
46
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
47 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your TMHMM install (ie the downloaded archive unzipped in `/path/to/tmhmm/2.0c/`):
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
48
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
49 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
50 binary.tmhmm.path=/path/to/tmhmm/2.0c/bin/decodeanhmm.Linux_x86_64
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
51 tmhmm.model.path=/path/to/tmhmm/2.0c/lib/TMHMM2.0.model
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
52 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
53
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
54 ### Phobius
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
55
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
56 Download Phobius from https://phobius.sbc.su.se/data.html
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
57
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
58 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your Phobius install (ie the downloaded archive unzipped in `/pth/to/phobiu/`):
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
59
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
60 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
61 binary.phobius.pl.path=/path/to/phobius/phobius.pl
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
62 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
63
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
64 Make sure the phobius.pl script begins like this:
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
65
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
66 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
67 #!/usr/bin/env perl
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
68 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
69
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
70 ### SMART data
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
71
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
72 Download SMART data from https://software.embl-em.de/software/18 (choose SMART 7.1)
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
73
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
74 Copy the THRESHOLDS file from the archive into `${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS`
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
75
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
76 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use this SMART file:
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
77
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
78 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
79 smart.threshold.path=${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
iuc
parents: 4
diff changeset
80 ```