On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning
<bjoern.gruen...@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
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