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This page last modified: Mar 07 2006
title:How to run SPC ISB tools.
description:How to run readw.exe, msxml2other.exe, dtafilter, sequest27.exe, out2summary, interact.

You must install cygwin and the SPC applications. However, the
instructions for running these are very misleading, and the scripts
that run other scripts have serious errors. Below are comments and the
commands that worked. Apparently this sequence of commands was
intended to be run by a shell script under cygwin. However, the shell
script doesn't work, and the commands themselves are fairly easy to
run (at least for a single run). If you do this many times, you'll
need to get a programmer to write you a shell script, or even a Perl
script (ActiveState makes a very nice free Perl for Windows).

You might consider these to be examples. 

(The authors of these scripts at SPC/ISB should feel free to contact me
to shed light on why the original scripts failed. The failures mostly
had to do with incorrect path assumptions and missing or incorrectly
named files within the scripts. The cygwin shell error messages made
it fairly easy for a Linux/Unix programmer (me) to guess the original
author's intentions and run the proper commands.)

#Create a .mzXML file from the .RAW file:

readw.exe 3stds.RAW c

# Try this command (my recollection is that the command
# is msxml2other.exe not msxml2other (without the .exe):

msxml2other.exe -dta 3stds.mzXML

# If msxml2other.exe does not create a folder 3stds, then create that
# folder manually and rerun msxml2other.exe

mkdir 3stds

# Copy the sequest.params file into the 3stds folder:

cp sequest.params 3stds/

# Change directory into the 3stds folder:

cd 3stds

# Filter (delete) dta files not meeting certain criteria:

dtafilter -A -P15

# Search all dta files. Here is a find command that should work:

find . -name "*.dta" -print | xargs /cygdrive/c/Xcalibur/system/programs/Bioworks.browser/sequest27.exe

# Create a summary 3stds.html file in the directory above 3stds:

out2summary . > ../3stds.html

# Change directory to the folder above 3stds:

cd ../

# Run Interact.