Issue msconvert (tool configuration?)

Workflow4Metabolomics Instance
1

Hi,

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)

"We trust you have received the usual lecture from the local System
Administrator. It usually boils down to these three things:

    #1) Respect the privacy of others.
    #2) Think before you type.
    #3) With great power comes great responsibility.

sudo: no tty present and no askpass program specified"

Any clue?
Best
Yann

2
3

Ping @team.w4m any idea about a potential misconfiguration on our instance for msconvert tool (sudo ?) ?

4

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.

5

Hi Mélanie,

Thank you for the details.

I alos reproduce this error on usegalaxy.fr instance.
Maybe @team.galaxy can help us resolve this issue ?

6

The msconvert Galaxy wrapper expect a dependency based on Docker:

It's something we don't support yet at usegalaxy.fr
I don't know if we can switch to a singularity image?

7

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 $*"