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ChromA - Maltcms Download
ChromA is based on the framework Maltcms (Modular Application
Toolkit for Chromatography-Mass Spectrometry), developed by Nils
Hoffmann, and is basically a web service frontend calling an
appropriately configured instance of Maltcms. The current release
of Maltcms is command-line only, but should non-the-less be easy
to use. If not, please post a bug to our bugtracker. Additionally, if you have ideas for
improvements or want to participate, do not hesitate to contact me directly.
Example files
Requirements for end usersBefore downloading the release
version, please make sure, that your system meets the following
requirements:
- Java SE
Runtime Environment (JRE) 6
- Alignment requires quadratic space in the worst case, so
for long chromatograms, make sure there is enough memory
installed. I recommend running Maltcms with a Heap Size of 2G
for chromatograms with about 5500 scans and 500 m/z bins, it
might also run with less memory, for smaller files. If you plan
to use any of the PairwiseAlignmentMatrixVisualizer class, 2G
might not be sufficient (it's an 5500x5500 image plus tics
plotted on top and to the left, plus additional space required
for the color legend and names of the chromatogram files).
Download
Maltcms Release
The wrapper scripts
assemble and then execute the following command line, which of
course can also be entered by hand, in the directory, where you
unzipped the maltcms-release.zip, change dir to maltcms and
enter:
java -Xmx 2G -Xms 1G -64
-Dlog4j.configuration=file://PATH/TO/MALTCMS/cfg/log4j.properties
-cp
/PATH/TO/MALTCMS/lib/maltcms-lib.jar:...:/PATH/TO/MALTCMS/lib/other.jar
apps.Maltcms
Please make sure, that all jar files contained within the lib
directory of the Maltcms release are contained on the classpath.
Running on Unix/Linux/MacOS X with bash compatible
shellMaltcms has been developed and tested mainly on SUN
Solaris, Ubuntu 8.04/8.10 Linux and MacOS X 10.5.6. For these
platforms, we use Shell scripts for the BASH shell to provide
additional command line happyness.
From the basedir of maltcms, enter:
scripts/maltcms-interactive.sh to start a script
asking you for the arguments to the command line, or enter:
scripts/maltcms.sh to start a script taking the
arguments directly as parameters. In order to get help on Maltcms
(not the wrapper script ;-)) and its input parameters,
type:
scripts/maltcms.sh -- -?.
Running on Windows (XP and later)Please note, that there
are currently no wrapper scripts for Maltcms available for
Windows. However, the main issue would be the construction of the
classpath argument to the program call, as given under General Remarks. Please let me know, whether you
are interested in having such wrapper scripts (batch files) for
Windows and I will see, what I can do about it.
Requirements for developers
Download
Maltcms Sources
Go to
project homepage on sourceforge
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