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comparison tool_dependencies.xml @ 110:fa6ef7619bbd draft default tip

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Uploaded
author bgruening
date Mon, 26 Jan 2015 13:10:16 -0500
parents 89dd3b812906
children
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109:89dd3b812906 110:fa6ef7619bbd
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <set_environment version="1.0"> 3 <package name="samtools" version="0.1.19">
4 <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> 4 <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </set_environment>
6 <package name="searchgui" version="1.18.0">
7 <repository changeset_revision="3bcfc0d7275b" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package> 5 </package>
9 <package name="peptide_shaker" version="0.28.0"> 6 <package name="numpy" version="1.9">
10 <repository changeset_revision="aa0a836dfaa9" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="c35b30122eb6" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 8 </package>
9 <package name="matplotlib" version="1.4">
10 <repository changeset_revision="6424ce261dab" name="package_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="scipy" version="0.14">
13 <repository changeset_revision="38e76888714c" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pysam" version="0.8.1">
16 <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="bx-python" version="0.7.2">
19 <repository changeset_revision="b9a2fe72b835" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
20 </package>
21 <package name="python" version="2.7">
22 <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
23 </package>
24 <package name="ucsc_tools" version="0.1">
25 <install version="1.0">
26 <actions>
27 <action type="download_binary">
28 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
29 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
30 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
31 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
32 </action>
33 <action type="chmod">
34 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
35 </action>
36 <action type="download_binary">
37 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
38 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
39 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
40 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
41 </action>
42 <action type="chmod">
43 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
44 </action>
45 <action type="download_binary">
46 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
47 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
48 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
49 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
50 </action>
51 <action type="chmod">
52 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
53 </action>
54 <action type="set_environment">
55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
56 </action>
57 </actions>
58 </install>
59 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
60 </package>
61
62 <package name="deepTools" version="1.5.9.1">
63 <install version="1.0">
64 <actions>
65 <action type="set_environment_for_install">
66 <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
67 <package name="pysam" version="0.8.1" />
68 </repository>
69 <repository changeset_revision="b9a2fe72b835" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
70 <package name="bx-python" version="0.7.2" />
71 </repository>
72 <repository changeset_revision="c35b30122eb6" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
73 <package name="numpy" version="1.9" />
74 </repository>
75 <repository changeset_revision="6424ce261dab" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
76 <package name="matplotlib" version="1.4" />
77 </repository>
78 <repository changeset_revision="38e76888714c" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
79 <package name="scipy" version="0.14" />
80 </repository>
81 </action>
82 <action type="setup_python_environment">
83 <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
84 <package name="python" version="2.7" />
85 </repository>
86 <!-- allow downloading and installing an Python package from https://pypi.org/ -->
87 <package>https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.9.1.tar.gz</package>
88 </action>
89
90 <action type="set_environment">
91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
92 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
93 <!-- disable the config file of deepTools -->
94 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
95 </action>
96 </actions>
97 </install>
98 <readme>
99 Installation of deepTools from Fidel Ramirez.
100 https://github.com/fidelram/deepTools
101 </readme>
102 </package>
12 </tool_dependency> 103 </tool_dependency>