Mercurial > repos > crs4 > edge_pro

comparison tool_dependencies.xml @ 3:ddcbf8732706 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
author crs4
date Mon, 19 Jan 2015 12:48:51 -0500
parents f77ce4f92b46
children
comparison
equal deleted inserted replaced
2:bad8a51514dd 3:ddcbf8732706
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="bowtie2" version="2.1.0"> 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" /> 4 <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="edge-pro" version="1.3.1"> 6 <package name="edge-pro" version="1.3.1">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <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>
10 <!-- Search executables in PATH instead of the CWD -->
11 <action type="shell_command">sed -i -e 's|$sourceDir/||' edge.pl</action>
10 <action type="shell_command">make</action> 12 <action type="shell_command">make</action>
11 <action type="move_file"> 13 <action type="move_file">
12 <source>count</source> 14 <source>count</source>
13 <destination>$INSTALL_DIR/bin</destination> 15 <destination>$INSTALL_DIR/bin</destination>
14 </action> 16 </action>