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:p.j.a.cock@googlemail.com] Envoyé : jeudi 12 novembre 2015 16:36 À : Björn Grüning <bjoern.gruening@gmail.com> Cc : Olivier CLAUDE <o.claude@outlook.fr>; galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning <bjoern.gruening@gmail.com> 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