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comparison tool_dependencies.xml @ 1:f77ce4f92b46 draft

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Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
author crs4
date Fri, 31 Jan 2014 05:44:03 -0500
parents 7af33315bc5e
children ddcbf8732706
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0:7af33315bc5e 1:f77ce4f92b46
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="bowtie2" version="2.1.0">
4 <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
3 <package name="edge-pro" version="1.3.1"> 6 <package name="edge-pro" version="1.3.1">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <actions>
6 <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action> 9 <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action>
7 <action type="shell_command">make</action> 10 <action type="shell_command">make</action>
12 <action type="move_file"> 15 <action type="move_file">
13 <source>edge.pl</source> 16 <source>edge.pl</source>
14 <destination>$INSTALL_DIR/bin</destination> 17 <destination>$INSTALL_DIR/bin</destination>
15 </action> 18 </action>
16 <action type="set_environment"> 19 <action type="set_environment">
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 20 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
18 </action> 21 </action>
19 </actions> 22 </actions>
20 </install> 23 </install>
21 <readme> 24 <readme>
22 Dependencies of EDGE-pro which needs to be installed separately: 25 Dependencies of EDGE-pro which needs to be installed separately:
23 - bowtie2 ( http://bowtie-bio.sourceforge.net/bowtie2/ ), in particular bowtie2, bowtie2-align and bowtie2-build need to be in the $PATH . These are usually already installed for Galaxy; 26 - Switch Perl module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
24 - Switch Perl core module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ). 27
28 Configuration: Previously (until Release 0), the EDGE_PRO_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--num-threads). This is not used anymore and may be removed.
25 </readme> 29 </readme>
26 </package> 30 </package>
27 </tool_dependency> 31 </tool_dependency>