Mercurial > repos > devteam > package_cufflinks_2_1_1

comparison tool_dependencies.xml @ 1:a8f40accd7ce draft default tip

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author devteam
date Fri, 19 Dec 2014 10:30:57 -0500
parents 394b13717223
children
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0:394b13717223 1:a8f40accd7ce
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="cufflinks" version="2.1.1"> 3 <package name="cufflinks" version="2.1.1">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions_group> 5 <actions_group>
6 <actions os="linux" architecture="x86_64"> 6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz</action> 7 <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz</action>
8 <action type="move_directory_files"> 8 <action type="move_directory_files">
9 <source_directory>.</source_directory> 9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR/bin</destination_directory> 10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
11 </action> 11 </action>
12 </actions> 12 </actions>
13 <actions os="darwin" architecture="x86_64"> 13 <actions architecture="x86_64" os="darwin">
14 <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz</action> 14 <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz</action>
15 <action type="move_directory_files"> 15 <action type="move_directory_files">
16 <source_directory>.</source_directory> 16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR/bin</destination_directory> 17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
18 </action> 18 </action>
19 </actions> 19 </actions>
20 <actions> 20 <actions>
21 <package name="boost" version="1.53.0"> 21 <package name="boost" version="1.53.0">
22 <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/" prior_installation_required="True" /> 22 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
23 </package> 23 </package>
24 <package name="samtools" version="0.1.18"> 24 <package name="samtools" version="0.1.18">
25 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" prior_installation_required="True" /> 25 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
26 </package> 26 </package>
27 <package name="eigen" version="3.2.0"> 27 <package name="eigen" version="3.2.0">
28 <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" prior_installation_required="True" /> 28 <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
29 </package> 29 </package>
30 <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.tar.gz</action> 30 <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.tar.gz</action>
31 <action type="set_environment_for_install"> 31 <action type="set_environment_for_install">
32 <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/" prior_installation_required="True"> 32 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
33 <package name="boost" version="1.53.0" /> 33 <package name="boost" version="1.53.0" />
34 </repository> 34 </repository>
35 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" prior_installation_required="True"> 35 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
36 <package name="samtools" version="0.1.18" /> 36 <package name="samtools" version="0.1.18" />
37 </repository> 37 </repository>
38 <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" prior_installation_required="True"> 38 <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39 <package name="eigen" version="3.2.0" /> 39 <package name="eigen" version="3.2.0" />
40 </repository> 40 </repository>
41 </action> 41 </action>
42 <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-boost=$BOOST_ROOT_DIR --with-bam=$BAM_ROOT --with-eigen=$EIGEN_ROOT</action> 42 <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-boost=$BOOST_ROOT_DIR --with-bam=$BAM_ROOT --with-eigen=$EIGEN_ROOT</action>
43 <action type="shell_command">make &amp;&amp; make install</action> 43 <action type="shell_command">make &amp;&amp; make install</action>
44 </actions> 44 </actions>
45 <action type="set_environment"> 45 <action type="set_environment">
46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
47 </action> 47 </action>
48 </actions_group> 48 </actions_group>
49 </install> 49 </install>
50 <readme></readme> 50 <readme />
51 </package> 51 </package>
52 </tool_dependency> 52 </tool_dependency>