Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 10:a68a771625d2 draft

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author bgruening
date Tue, 29 Oct 2013 17:26:28 -0400
parents 73761f33f198
children 46ddfceb1bb2
comparison
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9:73761f33f198 10:a68a771625d2
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.19"> 3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="18ccfc4b9542" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="numpy" version="1.7.1"> 6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="f0490401cfff" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="matplotlib" version="1.2.1"> 9 <package name="matplotlib" version="1.2.1">
10 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="scipy" version="0.12.0"> 12 <package name="scipy" version="0.12.0">
35 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template> 35 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
36 </action> 36 </action>
37 <action type="chmod"> 37 <action type="chmod">
38 <file mode="755">$INSTALL_DIR/bigWigInfo</file> 38 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
39 </action> 39 </action>
40 <action type="download_binary">
41 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
42 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
43 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
44 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
45 </action>
46 <action type="chmod">
47 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
48 </action>
40 <action type="set_environment"> 49 <action type="set_environment">
41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> 50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
42 </action> 51 </action>
43 </actions> 52 </actions>
44 </install> 53 </install>
45 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> 54 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
46 </package> 55 </package>
47 56
48 <package name="deepTools" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761"> 57 <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">
49 <install version="1.0"> 58 <install version="1.0">
50 <actions> 59 <actions>
60 <!-- populate the environment variables from the dependend repos -->
61 <action type="set_environment_for_install">
62 <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu">
63 <package name="pysam" version="0.7.5" />
64 </repository>
65 </action>
51 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> 66 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
52 <action type="shell_command">git reset --hard 3e13687c89e951476776b15afb4bbbc3b906f761</action> 67 <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action>
53 <action type="make_directory">$INSTALL_DIR/lib/python</action> 68 <action type="make_directory">$INSTALL_DIR/lib/python</action>
54 <action type="shell_command"> 69 <action type="shell_command">
55 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 70 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
56 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 71 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
57 </action> 72 </action>