fmaguire / wolfpsort Goto Github PK

If yes please add a few lines about it.

@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

Hi
I am new to Wolf psortb standalone version. Running the command
./bin/runWolfPsortSummary fungi < ./bin/testQuery.fasta
shows an error
./bin/wolfPredict: 1: ./bin/wolfPredict: Syntax error: "(" unexpected
Could you suggest a solution?
Thanks

Hi all,

I am trying to install WOLFPSort in order to run EffHunter on my university cluster command line. However, I am having trouble understanding how to install WOLFPSort, specially the first line found in the INSTALL document.

Please, do you have a more compleate guide on how to install it? I am not a bioinformatician and not very familiar with the command line. I have tried the git clone but apparently it fails to log in with username and password.

Hello fmaguire,
I installed your package on my Mac OS X 10.9.5 following your installation instructions and ran this command line:
runWolfPsortSummary fungi < Tools/WoLFPSort-master/bin/testQuery.fasta
An error appeared: wolfPredict: cannot execute binary file.
What have I to do?
On the other hand, I read in the README file that there is a script runWolfPsortSummaryOnly.pl in the bin directory. But, I don't find it ; just a script runWolfPsortSummary. Is it normal?
Thanks a lot for your help.
Laurence

I run the test data as:
./runWolfPsortSummary fungi <testQuery.fasta

The output is:

RCC1_YEAST nucl 12.5, mito_nucl 11.5, mito 9.5, cyto 3
RCL1_YEAST mito 15.5, cyto_mito 12.833, cyto 9, cyto_nucl 5.833
RT04_YEAST mito 16, nucl 8, cyto 3
EF1A_ASHGO cyto 27

It seems as if the result of RCL1_YEAST is wrong. In testQuery.fasta it shows that RCL1_YEAST is nucl, not mito. Other three are right.