Installation unclear - only works from source folder?

[peterjc]

@fmaguire I know this isn't your responsibility, I'm mainly posting this issue here to give it a little more visibility in the hope of helping others.

I had trouble getting runWolfPsortSummary to run unless I had first changed to its directory (e.g. /opt/WoLFPSORT_package_v0.2/bin on my machine). As a workaround, I created a short wrapper script to do that prior to running the tool:

#!/usr/bin/env python
#Wrapper script to call WoLF PSORT from its own directory.
import os
import sys
import subprocess
saved_dir = os.path.abspath(os.curdir)
os.chdir("/opt/WoLFPSORT_package_v0.2/bin")
args = ["./runWolfPsortSummary"] + sys.argv[1:]
return_code = subprocess.call(args)
os.chdir(saved_dir)
sys.exit(return_code)

See https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.py#L43 and this thread https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-December/023386.html

This could be down to my own mistake, not being a Perl expert, but it worked for me and is how I installed and used WoLF PSORT from Galaxy, see https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.xml and http://dx.doi.org/10.7717/peerj.167

[fmaguire]

Grand, I'll add a link to this in the install instructions (and add your wrapper script). Although if you want you are welcome to do a PR so it is correctly attributed to your github account.

[peterjc]

I'm still hoping there was something simple in the installation that I'd missed...