Mercurial > repos > devteam > package_tophat2_2_0_9

comparison tool_dependencies.xml @ 0:8549fd545473 draft default tip

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:24:58 -0500
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-1:000000000000 0:8549fd545473
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="tophat2" version="2.0.9">
4 <install version="1.0">
5 <actions_group>
6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.9.Linux_x86_64.tar.gz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
11 </action>
12 </actions>
13 <actions architecture="x86_64" os="darwin">
14 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/tophat/tophat-2.0.9.OSX_x86_64.tar.gz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
18 </action>
19 </actions>
20 <actions>
21 <package name="samtools" version="0.1.18">
22 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
23 </package>
24 <action type="download_by_url">http://tophat.cbcb.umd.edu/downloads/tophat-2.0.9.tar.gz</action>
25 <action type="set_environment_for_install">
26 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
27 </action>
28 <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-bam=$BAM_ROOT</action>
29 <action type="shell_command">make &amp;&amp; make install</action>
30 </actions>
31 <action type="set_environment">
32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
33 </action>
34 </actions_group>
35 </install>
36 <readme />
37 </package>
38 </tool_dependency>