|
2
|
1 <?xml version="1.0"?>
|
|
0
|
2 <tool_dependency>
|
|
|
3 <package name="samtools" version="0.1.18">
|
|
2
|
4 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
0
|
5 </package>
|
|
|
6 <package name="numpy" version="1.7.1">
|
|
7
|
7 <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
0
|
8 </package>
|
|
|
9 <package name="matplotlib" version="1.2.1">
|
|
7
|
10 <repository changeset_revision="a476c1177222" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
0
|
11 </package>
|
|
|
12 <package name="scipy" version="0.12.0">
|
|
7
|
13 <repository changeset_revision="710c8d9bb449" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
0
|
14 </package>
|
|
7
|
15 <package name="pysam" version="0.7.5">
|
|
|
16 <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
|
17 </package>
|
|
0
|
18 <package name="ucsc_tools" version="0.1">
|
|
|
19 <install version="1.0">
|
|
|
20 <actions>
|
|
|
21 <action type="download_binary">
|
|
2
|
22 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
|
|
|
23 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
|
|
|
24 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
|
|
|
25 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
|
|
0
|
26 </action>
|
|
|
27 <action type="chmod">
|
|
|
28 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
|
|
|
29 </action>
|
|
|
30 <action type="download_binary">
|
|
2
|
31 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
|
|
|
32 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
|
|
|
33 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
|
|
|
34 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
|
|
0
|
35 </action>
|
|
|
36 <action type="chmod">
|
|
|
37 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
|
|
|
38 </action>
|
|
|
39 <action type="set_environment">
|
|
2
|
40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
|
|
0
|
41 </action>
|
|
|
42 </actions>
|
|
|
43 </install>
|
|
|
44 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
|
|
|
45 </package>
|
|
|
46
|
|
6
|
47 <package name="deepTools" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">
|
|
0
|
48 <install version="1.0">
|
|
|
49 <actions>
|
|
7
|
50 <!-- populate the environment variables from the dependend repos -->
|
|
|
51 <action type="set_environment_for_install">>
|
|
|
52 <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
|
53 <package name="pysam" version="0.7.5" />
|
|
|
54 </repository>
|
|
|
55 </action>
|
|
0
|
56 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
|
|
6
|
57 <action type="shell_command">git reset --hard df852fa1ef13251a17274ee18fbf919fbc515079</action>
|
|
0
|
58 <action type="make_directory">$INSTALL_DIR/lib/python</action>
|
|
|
59 <action type="shell_command">
|
|
7
|
60 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python: &&
|
|
0
|
61 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
|
|
|
62 </action>
|
|
|
63
|
|
|
64 <action type="set_environment">
|
|
2
|
65 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
|
|
|
66 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
|
|
1
|
67 <!-- disable the config file of deepTools -->
|
|
2
|
68 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
|
|
0
|
69 </action>
|
|
|
70 </actions>
|
|
|
71 </install>
|
|
|
72 <readme>Installation of deepTools from Fidel Ramirez.</readme>
|
|
|
73 </package>
|
|
|
74 </tool_dependency>
|
