search

peterjc / pico_galaxy

Galaxy tools and wrappers for sequence analysis
17 stars 25 forks source link

Capture version of Promoter 2, NOD, WoLF PSORT #8

Closed peterjc closed 7 years ago

peterjc commented 9 years ago

Reported by @peterthorpe5

peterjc commented 9 years ago

Also missing <version_command> in other tools, e.g. tmhmm2.xml and signalp.xml

Notes:

$ java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector"
NucleOlar localization sequence Detector v. 1.3b (13 May 2011) 
$ promoter -V
promoter 2.0a, May 2001, revised in Aug 2004

Tricky ones:

$ grep "is version" ~/bin/tmhmm 
# This is version 2.0c of tmhmm

This comment appears to be the only version indicator.

$ head ~/bin/signalp
#!/bin/sh

# SignalP 3.0a, May 2004
# 
# VERSIONS  3.0a    18 May 2004 launch
#       3.0b    15 Dec 2005 bugfixes, see README
# 

SYSTEM=`uname -s`           # which platform?

(That was probably SignalP 3.0b but the text is inconsistent)

$ head /opt/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary 
#!/usr/bin/perl -w
#
#  Author: Paul Horton (remnants of code from CJ Collier may remain).
#  Maintainer: Paul Horton.
#  Organization: Computational Biology Research Center, AIST, Japan
#  Creation Date: Summer 2004
#  Last Modification $Date: 2006/08/31 07:21:44 $
#  Copyright: Paul Horton
#  Licensing: Anyone may distribute this under the GNU public license. For other
#             license information contact: horton-p AT aist.go.jp

There doesn't seem to be a version, so use stated last modified date instead?

peterjc commented 9 years ago

Having fixed clinod and promoter2, I'm going to close this issue.

Sadly none of tmhmm2, signapl3 and WoLF-PSOST provide a simple way to reliably determine their version.

peterthorpe5 commented 9 years ago

OK. Nice work Pete

peterjc commented 9 years ago

As an aside, I found a Galaxy bug in the parallelism feature during this work: https://trello.com/c/PCjHetBw/2745-tool-versions-not-captured-if-using-parallelism-use-tasked-jobs

If use_tasked_jobs = False then the <version_command> tag is run prior to the <command> tag as expected.

If use_tasked_jobs = True then it appears that after splitting the input, none of the child-jobs include the <version_command>.

peterjc commented 7 years ago

Actually closing issue.