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annotate README.md @ 11:98cafcbd2578 draft

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"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
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fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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1 # InterProScan
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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3 ## Licensed software/data
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fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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5 The standard install of InterProScan does not include the following components, because their license does not allow redistribution:
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fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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7 - SignalP
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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8 - TMHMM
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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9 - Phobius
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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10 - SMART data (THRESHOLD file)
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fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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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.
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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14 ## Installing licensed components manually
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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16 All the following steps assume that:
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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18 - You agree with each software license
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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19 - InterProScan was installed using Conda in the `IPRSCAN_DIR` directory
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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/`)
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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22 Everytime you upgrade InterProScan, you'll need to do the same things: modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file + add the SMART file.
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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24 ### SignalP
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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26 Download and install SignalP 4.1 from https://services.healthtech.dtu.dk/service.php?SignalP-4.1
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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28 Modify the `${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"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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30 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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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"
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32 signalp.perl.library.dir=/path/to/signalp/4.1/lib/
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33 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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35 Make sure the SignalP script begins like this:
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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37 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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38 #!/usr/bin/env perl
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39 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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41 And make sure, you have properly set `$ENV{SIGNALP}` in the SignalP script (around line 13).
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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43 ### TMHMM
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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45 Download and install TMHMM 2.0c from https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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47 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your TMHMM install (ie the downloaded archive unzipped in `/path/to/tmhmm/2.0c/`):
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49 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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50 binary.tmhmm.path=/path/to/tmhmm/2.0c/bin/decodeanhmm.Linux_x86_64
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51 tmhmm.model.path=/path/to/tmhmm/2.0c/lib/TMHMM2.0.model
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52 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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54 ### Phobius
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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56 Download Phobius from https://phobius.sbc.su.se/data.html
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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58 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use your Phobius install (ie the downloaded archive unzipped in `/pth/to/phobiu/`):
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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60 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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61 binary.phobius.pl.path=/path/to/phobius/phobius.pl
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62 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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64 Make sure the phobius.pl script begins like this:
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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66 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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67 #!/usr/bin/env perl
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68 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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70 ### SMART data
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72 Download SMART data from https://software.embl-em.de/software/18 (choose SMART 7.1)
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74 Copy the THRESHOLDS file from the archive into `${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS`
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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76 Modify the `${IPRSCAN_DIR}/share/InterProScan/interproscan.properties` file to use this SMART file:
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c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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78 ```
c55643c3d813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
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79 smart.threshold.path=${IPRSCAN_DATA_DIR}/data/smart/7.1/THRESHOLDS
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80 ```