UsefulScripts

scripts courtesy of pieter DOT kelchtermans AT ugent.be

Use wine to convert raw files

wine /home/compomics/.wine/drive_c/Program\ Files/ProteoWizard/ProteoWizard\ 3.0.4323/msconvert.exe "$@"

Use OpenMS tools like a linux tool

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#!/bin/zsh # This script makes OpenMS tools accept stdin input and stdout output (to chain them as normal Unix tools) if [ $# -eq 0 ] ; then echo "usage: $0 OpenmsTool -ini OpenmsTool.ini < infile > outfile" exit 0 fi # You'll want to have a tmpfs (RAM + SWAP if needed) disk configured with about half the size of your RAM in /etc/fstab: tmpfs /tmp tmpfs defaults,noatime,mode=1777,nosuid,size=16G 0 0 # This makes for very fast access speeds, in this case for a file collection up to about 16GB. This script makes the OpenMS tools write only to this RAM-disk, and then outputs that file to stdout # Since /tmp is configured to be a RAM(+SWAP)-disk, let's create a random directory, TDIR=$(mktemp -d) # and make sure it gets deleted even if this script terminates unexpectedly. trap "{ cd - ; rm -rf $TDIR; exit 255; }" SIGINT # ${cat} reads stdin (binary and text data), this is then echoed into a file called "in", in this fast tmp directory echo "$(cat)" > $TDIR/in # $@ are the arguments of this tool, which should be equivalent to the OpenMS line you'd normally use, minus the -in and -out parameters, since those now point to temporary files on a ramdisk # also redirect OpenMS stdout log messages to stderr, we only want the outfile on stdout of this script # when the tool completes successfully, spew the outfile to stdout with cat "$@" -in $TDIR/in -out $TDIR/out 1>&2 && cat $TDIR/out # remove the temporary directory with everything in it rm -rf $TDIR # and get the hell out of here! exit 0