Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 2:4762b84d13f5 draft

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author bgruening
date Mon, 05 Aug 2013 10:11:32 -0400
parents 21d563d5f2b2
children 522686bcd5c0
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1:21d563d5f2b2 2:4762b84d13f5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <!--
3
4 <requirement type="package">deepTools</requirement>
5 <requirement type="python-module">deepTools</requirement>
6 <requirement type="python-module">matplotlib</requirement> -> toolshed
7 <requirement type="python-module">argsparse</requirement> -> is in python 2.7 or?
8 <requirement type="python-module">itertools</requirement> -> is in standard python?
9 <requirement type="python-module">pysam</requirement> -> is also shipped with galaxy
10 <requirement type="python-module">numpy</requirement> -> toolshed
11 <requirement type="python-module">pylab</requirement> -> scipy toolshed
12 <requirement type="python-module">bx.intervals.io</requirement> -> bx-python is shipped with galaxy afaik
13 -->
14
15 <tool_dependency> 2 <tool_dependency>
16 <package name="samtools" version="0.1.18"> 3 <package name="samtools" version="0.1.18">
17 <repository name="package_samtools_0_1_18" owner="devteam" /> 4 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
18 </package> 5 </package>
19 <package name="numpy" version="1.7.1"> 6 <package name="numpy" version="1.7.1">
20 <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" /> 7 <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
21 </package> 8 </package>
22 <package name="matplotlib" version="1.2.1"> 9 <package name="matplotlib" version="1.2.1">
23 <repository name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" /> 10 <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
24 </package> 11 </package>
25 <package name="scipy" version="0.12.0"> 12 <package name="scipy" version="0.12.0">
26 <repository name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" /> 13 <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
27 </package> 14 </package>
28 15
29 <package name="ucsc_tools" version="0.1"> 16 <package name="ucsc_tools" version="0.1">
30 <install version="1.0"> 17 <install version="1.0">
31 <actions> 18 <actions>
32 <action type="download_binary"> 19 <action type="download_binary">
33 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> 20 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
34 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> 21 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
35 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> 22 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
36 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template> 23 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
37 </action> 24 </action>
38 <action type="chmod"> 25 <action type="chmod">
39 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file> 26 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
40 </action> 27 </action>
41 <action type="download_binary"> 28 <action type="download_binary">
42 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template> 29 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
43 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template> 30 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
44 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template> 31 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
45 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template> 32 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
46 </action> 33 </action>
47 <action type="chmod"> 34 <action type="chmod">
48 <file mode="755">$INSTALL_DIR/bigWigInfo</file> 35 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
49 </action> 36 </action>
50 <action type="set_environment"> 37 <action type="set_environment">
51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> 38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
52 </action> 39 </action>
53 </actions> 40 </actions>
54 </install> 41 </install>
55 <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> 42 <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>
56 </package> 43 </package>
65 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 52 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
66 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 53 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
67 </action> 54 </action>
68 55
69 <action type="set_environment"> 56 <action type="set_environment">
70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 57 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
71 <environment_variable name="PYTHONPATH" action="append_to" >$INSTALL_DIR/lib/python</environment_variable> 58 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
72 <!-- disable the config file of deepTools --> 59 <!-- disable the config file of deepTools -->
73 <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable> 60 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
74 </action> 61 </action>
75 </actions> 62 </actions>
76 </install> 63 </install>
77 <readme>Installation of deepTools from Fidel Ramirez.</readme> 64 <readme>Installation of deepTools from Fidel Ramirez.</readme>
78 </package> 65 </package>