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comparison tool_dependencies.xml @ 17:35a80f8dda5c draft

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author iuc
date Sat, 15 Feb 2014 15:43:39 -0500
parents d9a0a017896a
children 05aca18fd8dc
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16:d9a0a017896a 17:35a80f8dda5c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 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"> 3 <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" /> 4 <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" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package> 5 </package>
12 <package name="scipy" version="0.12.0"> 6 <package name="scipy" version="0.12.0">
13 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
14 </package> 8 </package>
15 <package name="pysam" version="0.7.7"> 9 <package name="R_3_0_1" version="3.0.1">
16 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
17 </package> 11 </package>
18 <package name="bx-python" version="12-2013"> 12 <package name="gnu_awk" version="4.1.0">
19 <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
20 </package> 14 </package>
21 15 <set_environment version="1.0">
22 <package name="ucsc_tools" version="0.1"> 16 <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
17 </set_environment>
18 <!-- 2.0.10 12162013 -->
19 <package name="macs2" version="2.0.10.3">
23 <install version="1.0"> 20 <install version="1.0">
24 <actions> 21 <actions>
25 <action type="download_binary"> 22 <action type="shell_command">git clone --recursive https://github.com/taoliu/MACS.git</action>
26 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> 23 <!-- Galaxy tries to change automatically to the directory "macs2" (name of the package).
27 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> 24 But we need to change to MACS. Go one level back and enter MACS -->
28 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> 25 <action type="change_directory">../MACS</action>
29 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template> 26 <action type="shell_command">git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb</action>
30 </action> 27 <action type="shell_command">git submodule update --recursive</action>
31 <action type="chmod">
32 <file mode="755">$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 28
60 <package name="deepTools" version="1.5.4_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">
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"> 29 <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="5457e32b427c" 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 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 30 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
73 <package name="numpy" version="1.7.1" /> 31 <package name="numpy" version="1.7.1" />
74 </repository>
75 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
76 <package name="matplotlib" version="1.2.1" />
77 </repository> 32 </repository>
78 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 33 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
79 <package name="scipy" version="0.12.0" /> 34 <package name="scipy" version="0.12.0" />
80 </repository> 35 </repository>
81 </action> 36 </action>
82 <action type="shell_command">git reset --hard 3268f7e1458f3a520ab6fea3039971ee9d7a6d5b</action>
83 <action type="make_directory">$INSTALL_DIR/lib/python</action> 37 <action type="make_directory">$INSTALL_DIR/lib/python</action>
84 <action type="shell_command"> 38 <action type="shell_command">
85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 39 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
86 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 40 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
87 </action> 41 </action>
88 <action type="set_environment"> 42 <action type="set_environment">
43 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
44 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
45 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
89 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
90 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 47 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
91 <!-- disable the config file of deepTools --> 48 <environment_variable action="set_to" name="PYTHONPATH_MACS2">$INSTALL_DIR/lib/python</environment_variable>
92 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> 49 </action>
93 </action> 50 </actions>
94 </actions> 51 </install>
95 </install> 52 <readme>Macs2 installation instructions. MACS2 can be found at https://github.com/taoliu/MACS</readme>
96 <readme> 53 </package>
97 Installation of deepTools from Fidel Ramirez.
98 https://github.com/fidelram/deepTools
99 </readme>
100 </package>
101 </tool_dependency> 54 </tool_dependency>