I have tried to run a MS file conversion on workflow4metabolomics.usegalaxy.fr but it crashed.
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2
I think of a configuration issue on our instance as it worked on usegalaxy.eu. msconvert Convert and/or filter mass spectrometry files (Galaxy Version 3.0.20287.2)
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Hi there,
This Galaxy tool is not supported by W4M, I am not sure someone from the W4M team has experience with it in an admin/code way.
All I have is that one of my colleague confirmed that the same version of the tool on usegalaxy.eu is running fine. She tested the two of them yesterday because she would have appreciate to use it in usegalaxy.fr instead of usegalaxy.eu for an upcomming training session about Metabolomics.
I have already used a Singularity image using chambm/pwiz-skyline-i-agree-to-the-vendor-licenses docker image.
But it was a little bit tricky cause "wineprefix" directory (and I didn't find a simple way)
Here the modulefile used (and the installation)
#%Module -*- tcl -*-
###########################
## Proteowizard msconvert
###########################
## INSTALLATION
#
# mkdir -p /module/apps/msconvert/3.0.20239-db48a3d0d
# cd /module/apps/msconvert/3.0.20239-db48a3d0d
# mkdir mywineprefix
#
# singularity exec -B mywineprefix:/mywineprefix docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses /bin/bash cp -ra /wineprefix64/* /mywineprefix/
#
# Test
# singularity exec -B mywineprefix:/mywineprefix docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses mywine msconvert --help
## ----------------------------------------------
## Description
## ----------------------------------------------
set descr "Proteowizard msconvert"
append descr "\nhttps://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses/"
module-whatis "Adds [module-info name] environment.\n$descr"
proc ModulesHelp { } {
global descr
puts stderr "$descr\n"
}
## Definition de variables internes au modulefile
## ----------------------------------------------
set name msconvert
set version 3.0.20239-db48a3d0d
set prefix /module/apps/${name}/${version}
## Protection permettant de verifier la presence du PATH precedent
## ---------------------------------------------------------------
if {![file exists $prefix]} {
puts stderr "\t[module-info name] Load Error: $prefix does not exist"
break
exit 1
}
# Ajout des PATH
# ---------------------------------------
if [ module-info mode load ] {
puts stderr "You have read and accepted the license agreements:"
puts stderr "http://proteowizard.sourceforge.net/licenses.html"
puts stderr ""
puts stderr "Please cite the software in your publications"
puts stderr "http://proteowizard.sourceforge.net/download.html"
puts stderr ""
if {![file exists "~/.wine-msconvert"]} {
puts stderr "Create wine environement (~/.wine-msconvert)..."
file copy $prefix/mywineprefix ~/.wine-msconvert
puts stderr "... done"
puts stderr ""
}
}
set-alias msconvert "singularity exec -B ~/.wine-msconvert:/mywineprefix docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses mywine msconvert $*"