Mercurial > repos > iracooke > protk_msgfplus
changeset 7:a8ae51506967
Updated dependency info
author | iracooke |
---|---|
date | Mon, 04 Mar 2013 23:59:59 -0500 (2013-03-05) |
parents | 87757d28e0d2 |
children | 21c7f6a61d61 |
files | README repository_dependencies.xml tool_dependencies.xml |
diffstat | 3 files changed, 48 insertions(+), 18 deletions(-) [+] |
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--- a/README Mon Mar 04 21:43:23 2013 -0500 +++ b/README Mon Mar 04 23:59:59 2013 -0500 @@ -1,6 +1,42 @@ -This package is an installer for the MSGF+ search tool. +This package is an installer for BLAST+ from NCBI + +Requirements: +This package depends on the galaxy_protk package +Please see instructions for the galaxy_protk package before installing + +-------- ABOUT -------------- + +BLAST Command Line Applications + +The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of +local similarity between sequences. The program compares nucleotide or +protein sequences to sequence databases and calculates the statistical +significance of matches. BLAST can be used to infer functional and +evolutionary relationships between sequences as well as help identify +members of gene families. + +For more information, visit http://blast.ncbi.nlm.nih.gov + -System Requirements. Ensure that you have the following packages installed on your system -- unzip -- java runtime 6 or higher +-------- LICENCE ------------ + + + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information + This software/database is a "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 United States Government employee and + thus cannot be copyrighted. This software/database is freely available + to the public for use. The National Library of Medicine and the U.S. + Government have not placed any restriction on its use or reproduction. + + Although all reasonable efforts have been taken to ensure the accuracy + and reliability of the software and data, the NLM and the U.S. + Government do 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 disclaim all warranties, express or implied, including + warranties of performance, merchantability or fitness for any particular + purpose. + + Please cite the author in any work or product based on this material.
--- a/repository_dependencies.xml Mon Mar 04 21:43:23 2013 -0500 +++ b/repository_dependencies.xml Mon Mar 04 23:59:59 2013 -0500 @@ -1,10 +1,4 @@ <?xml version="1.0"?> -<!-- <repositories description="protk-msgfplus requires the protk rubygem to install MSGF+"> - <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="2562efef05cb"/> -</repositories> - --> - - - <repositories description="Requires the protk rubygem to install MSGF+"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/> + <repositories description="Requires the protk rubygem to perform the install"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> </repositories> \ No newline at end of file
--- a/tool_dependencies.xml Mon Mar 04 21:43:23 2013 -0500 +++ b/tool_dependencies.xml Mon Mar 04 23:59:59 2013 -0500 @@ -1,22 +1,22 @@ <?xml version="1.0"?> <tool_dependency> - <package name="msgfplus" version="20130227"> + <package name="blast" version="2.2.27"> <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_msgfplus.sh $INSTALL_DIR 1.1.9</action> + <action type="shell_command">sh install_blast.sh $INSTALL_DIR 1.2.0</action> <action type="move_file"> - <source>install_msgfplus.sh</source> + <source>install_blast.sh</source> <destination>$INSTALL_DIR</destination> </action> <action type="set_environment"> - <environment_variable name="PROTK_MSGFPLUS_ROOT" action="set_to">$INSTALL_DIR</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PROTK_BLAST_ROOT" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> - Installs MSGF+ via the protk installer + Installs BLAST via the protk installer </readme> </package>