I followed the instuctions given by peter and signalp works with galaxy! Thanks a lot! Do I try the same for tmhmm2 and promoter2? Thanks a lot again!
Olivier -----Message d'origine----- De : Peter Cock [mailto:[email protected]] Envoyé : jeudi 12 novembre 2015 16:36 À : Björn Grüning <[email protected]> Cc : Olivier CLAUDE <[email protected]>; galaxy-dev <[email protected]> Objet : Re: [galaxy-dev] Tmhmm and signal P On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning <[email protected]> wrote: > Hi, > > please make also sure the /bin directory inside of the signalp folder > is in your PATH. > > Things like combine-hmm-plp.awk should be included. > > Ciao, > Bjoern Thanks Bjorn, You don't need put that on the path, alternatively you can edit the SIGNALP=... line near the start of the signalp script - it defaults to /usr/opt/signalp-3.0/bin What we do is have a symbolic link (which is on the path) which points to the main script under /usr/opt/ or similar. These are my colleague's notes: <quote> SIGNALP arrives as the compressed file signalp-3.0.Linux.tar.Z, which can be uncompressed as usual: $ tar -zxvf signalp-3.0.Linux.tar.Z The resulting directory should be copied to /usr/opt/signalp-3.0 (this location is assumed by the SIGNALP scripts), and a symbolic link added to /usr/local/bin to enable command-line use. We also need to make the /usr/opt/signalp-3.0/tmp directory world-writable so that SIGNALP will run. $ sudo cp -R signalp-3.0/ /usr/opt/ $ sudo ln -s /usr/opt/signalp-3.0/signalp /usr/local/bin $ sudo chmod 777 /usr/opt/signalp-3.0/tmp </quote> If you don't have sudo rights, a little more work is needed. We currently use $HOME/opt/signalp-3.0/ and $HOME/bin/signalp as a symlink to /mnt/galaxy/opt/signalp-3.0/signalp but this requires you edit the script line to record the alternative path as the SIGNALP variable. Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
