Mercurial > repos > iracooke > protk_omssa

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Thu Jun 06 01:30:57 2013 -0400
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+This package installs the OMSSA MS/MS search engine
+
+Full details about OMSSA including a paper describing its algorithm
+can be found at http://pubchem.ncbi.nlm.nih.gov/omssa/
+
+Requirements:
+This package depends on the galaxy_protk package
+Please see instructions for that package before installing
+
+
+--- DISCLAIMER ----
+
+National Library of Medicine disclaimer:
+http://www.ncbi.nlm.nih.gov/About/disclaimer.html
+
+NCBI source code disclaimer:
+   **************************************************************************
+   *                                                                        *
+   *              National Center for Biotechnology Information             *
+   *       Bldg. 38A, NIH,  8600 Rockville Pike,  Bethesda, MD  20894       *
+   *                                                                        *
+   *                             COPYRIGHT NOTICE                           *
+   *                                                                        *
+   * This software/database is "United States Government Work" under the    *
+   * terms of the United States Copyright Act.  It was written as part of   *
+   * the author's official duties as a Government employee and thus cannot  *
+   * be copyrighted.  This software/database is freely available to the     *
+   * public for use without a copyright notice.  Restrictions cannot be     *
+   * placed on its present or future use.                                   *
+   *                                                                        *
+   * Although all reasonable efforts have been taken to ensure the accuracy *
+   * and reliability of the software and data, the National Library of      *
+   * Medicine (NLM) and the U.S. Government does not and cannot warrant the *
+   * performance or results that may be obtained by using this software or  *
+   * data.  The NLM and the U.S. Government disclaims all warranties as to  *
+   * performance, merchantability or fitness for any particular purpose.    *
+   *                                                                        *
+   * In any work or product derived from this material, proper attribution  *
+   * of the author as the source of the software or data would be           *
+   * appreciated.                                                           *
+   *                                                                        *
+   **************************************************************************
+
+OMSSA Citation:
+Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH.  "Open mass spectrometry search algorithm." J Proteome Res. 2004 Sep-Oct;3(5):958-64.
+
+http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15473683
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 06 01:30:57 2013 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="galaxy_protk" version="1.2.0">
+         <repository toolshed="http://10.211.55.35:9009" name="galaxy_protk" owner="iracooke" changeset_revision="0a2b3dcc986c" prior_installation_required="True"/>
+    </package>
+    <package name="omssa" version="2.1.9">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://dl.dropbox.com/u/226794/galaxy_protk.tar.gz</action>
+                <action type="shell_command">sh install_omssa.sh $INSTALL_DIR 1.2.0</action>
+                <action type="move_file">
+                    <source>install_omssa.sh</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PROTK_OMSSA_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installs OMSSA via the protk installer
+            By default OMSSA will run with as many threads as are available.
+            You can limit the number of threads by setting the environment
+            variable PROTK_OMSSA_NTHREADS to the number of threads you would like OMSSA to use.
+            Please see http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
+            for details on setting environment variables for galaxy tools
+        </readme>
+    </package>
+
+</tool_dependency>