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comparison tool_dependencies.xml @ 6:5742b322f956 draft default tip

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author greg
date Tue, 10 Dec 2013 10:09:39 -0500
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5:a80606f72321 6:5742b322f956
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" prior_installation_required="True" 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" prior_installation_required="True" 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" prior_installation_required="True" 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" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pysam" version="0.7.7">
16 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="bx-python" version="12-2013">
19 <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
20 </package>
21
22 <package name="ucsc_tools" version="0.1">
23 <install version="1.0">
24 <actions>
25 <action type="download_binary">
26 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
27 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
28 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
29 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
30 </action>
31 <action type="chmod">
32 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
33 </action>
34 <action type="download_binary">
35 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
36 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
37 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
38 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
39 </action>
40 <action type="chmod">
41 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
42 </action>
43 <action type="download_binary">
44 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
45 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
46 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
47 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
48 </action>
49 <action type="chmod">
50 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
51 </action>
52 <action type="set_environment">
53 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
54 </action>
55 </actions>
56 </install>
57 <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>
58 </package>
59
60 <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">
61 <install version="1.0">
62 <actions>
63 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
64 <!-- populate the environment variables from the dependend repos -->
65 <action type="set_environment_for_install">
66 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
67 <package name="pysam" version="0.7.7" />
68 </repository>
69 <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
70 <package name="bx-python" version="12-2013" />
71 </repository>
72 </action>
73 <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action>
74 <action type="make_directory">$INSTALL_DIR/lib/python</action>
75 <action type="shell_command">
76 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
77 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
78 </action>
79 <action type="set_environment">
80 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
81 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
82 <!-- disable the config file of deepTools -->
83 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
84 </action>
85 </actions>
86 </install>
87 <readme>
88 Installation of deepTools from Fidel Ramirez.
89 https://github.com/fidelram/deepTools
90 </readme>
91 </package>
92 </tool_dependency>