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comparison tool_dependencies.xml @ 0:03e5e7b2cedd draft default tip

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author devteam
date Thu, 14 Nov 2013 15:58:04 -0500
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-1:000000000000 0:03e5e7b2cedd
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package>
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" />
11 </package>
12 <package name="scipy" version="0.12.0">
13 <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pysam" version="0.7.6">
16 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
17 </package>
18
19 <package name="ucsc_tools" version="0.1">
20 <install version="1.0">
21 <actions>
22 <action type="download_binary">
23 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
24 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
25 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
26 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
27 </action>
28 <action type="chmod">
29 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
30 </action>
31 <action type="download_binary">
32 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
33 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
34 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
35 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
36 </action>
37 <action type="chmod">
38 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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">$INSTALL_DIR/bigWigToBedGraph</file>
48 </action>
49 <action type="set_environment">
50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
51 </action>
52 </actions>
53 </install>
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>
55 </package>
56
57 <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">
58 <install version="1.0">
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>
66 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
67 <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action>
68 <action type="make_directory">$INSTALL_DIR/lib/python</action>
69 <action type="shell_command">
70 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
71 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
72 </action>
73
74 <action type="set_environment">
75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
76 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
77 <!-- disable the config file of deepTools -->
78 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
79 </action>
80 </actions>
81 </install>
82 <readme>Installation of deepTools from Fidel Ramirez.</readme>
83 </package>
84 </tool_dependency>