Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children 7889d260cc37
comparison
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29:3a2aab18a217 30:5231f398d784
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="python" version="2.7">
4 <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="numpy" version="1.7.1"> 6 <package name="deepTools" version="1.5.11">
7 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="01eb49da8dcf" name="package_python_2_7_deeptools_1_5_11" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="matplotlib" version="1.2.1">
10 <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="scipy" version="0.12.0">
13 <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pysam" version="0.7.7">
16 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="bx-python" version="12-2013">
19 <repository changeset_revision="55bd96a1c3b3" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="1.5.9.1">
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="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
67 <package name="pysam" version="0.7.7" />
68 </repository>
69 <repository changeset_revision="55bd96a1c3b3" name="package_bx_python_12_2013" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
70 <package name="bx-python" version="12-2013" />
71 </repository>
72 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
73 <package name="numpy" version="1.7.1" />
74 </repository>
75 <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
76 <package name="matplotlib" version="1.2.1" />
77 </repository>
78 <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
79 <package name="scipy" version="0.12.0" />
80 </repository>
81 </action>
82 <action type="shell_command">git reset --hard 351890e3db9a443484c5c349791b7247163cc94f</action>
83 <action type="make_directory">$INSTALL_DIR/lib/python</action>
84 <action type="shell_command">
85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
86 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
87 </action>
88 <action type="set_environment">
89 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
90 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
91 <!-- disable the config file of deepTools -->
92 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
93 </action>
94 </actions>
95 </install>
96 <readme>
97 Installation of deepTools from Fidel Ramirez.
98 https://github.com/fidelram/deepTools
99 </readme>
100 </package>
101 </tool_dependency> 9 </tool_dependency>