Mercurial > repos > fcaramia > jointsnvmix
comparison tool_dependencies.xml @ 0:a1034918ab9b draft
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author | fcaramia |
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date | Thu, 20 Jun 2013 00:03:08 -0400 |
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children | 7fb20f2d156c |
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-1:000000000000 | 0:a1034918ab9b |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 | |
4 <package name="samtools" version="0.1.18"> | |
5 <install version="1.0"> | |
6 <actions> | |
7 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
8 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
9 <action type="shell_command">make</action> | |
10 <action type="move_file"> | |
11 <source>samtools</source> | |
12 <destination>$INSTALL_DIR/bin</destination> | |
13 </action> | |
14 <action type="move_file"> | |
15 <source>misc/maq2sam-long</source> | |
16 <destination>$INSTALL_DIR/bin</destination> | |
17 </action> | |
18 <action type="set_environment"> | |
19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
20 </action> | |
21 </actions> | |
22 </install> | |
23 <readme> | |
24 Compiling SAMtools requires the ncurses and zlib development libraries. | |
25 </readme> | |
26 </package> | |
27 | |
28 <package name="python" version="2.7"> | |
29 <readme> | |
30 JointSNVMix requires Python >= 2.7 | |
31 </readme> | |
32 </package> | |
33 | |
34 <package name="cython" version="0.19.1"> | |
35 <install version="1.0"> | |
36 <actions> | |
37 <action type="download_by_url">http://cython.org/release/Cython-0.19.1.tar.gz</action> | |
38 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
39 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> | |
40 <action type="set_environment"> | |
41 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> | |
42 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
43 </action> | |
44 </actions> | |
45 </install> | |
46 <readme> | |
47 </readme> | |
48 </package> | |
49 | |
50 <package name="pysam" version="0.5"> | |
51 <install version="1.0"> | |
52 <actions> | |
53 <action type="download_by_url">http://pysam.googlecode.com/files/pysam-0.5.tar.gz</action> | |
54 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
55 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> | |
56 <action type="set_environment"> | |
57 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> | |
58 </action> | |
59 </actions> | |
60 </install> | |
61 <readme> | |
62 </readme> | |
63 </package> | |
64 <package name="jointsnvmix" version="0.7.5"> | |
65 <install version="1.0"> | |
66 <actions> | |
67 <action type="download_by_url">http://joint-snv-mix.googlecode.com/files/JointSNVMix-0.7.5.tar.gz</action> | |
68 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
69 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> | |
70 <action type="set_environment"> | |
71 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> | |
72 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
73 </action> | |
74 </actions> | |
75 </install> | |
76 <readme> | |
77 </readme> | |
78 </package> | |
79 | |
80 | |
81 | |
82 </tool_dependency> |