Mercurial > repos > fcaramia > contra
comparison tool_dependencies.xml @ 23:2770f49cb0dc
re-uploading contra
author | Franco Caramia <franco.caramia@petermac.org> |
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date | Tue, 20 May 2014 09:59:00 +1000 |
parents | |
children | c361b3fb806e |
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22:e8a98923965e | 23:2770f49cb0dc |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="samtools" version="0.1.18"> | |
4 <install version="1.0"> | |
5 <actions> | |
6 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
7 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
8 <action type="shell_command">make</action> | |
9 <action type="move_file"> | |
10 <source>samtools</source> | |
11 <destination>$INSTALL_DIR/bin</destination> | |
12 </action> | |
13 <action type="move_file"> | |
14 <source>misc/maq2sam-long</source> | |
15 <destination>$INSTALL_DIR/bin</destination> | |
16 </action> | |
17 <action type="set_environment"> | |
18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
19 </action> | |
20 </actions> | |
21 </install> | |
22 <readme> | |
23 Compiling SAMtools requires the ncurses and zlib development libraries. | |
24 </readme> | |
25 </package> | |
26 | |
27 | |
28 <package name="bedtools" version="2.17.0"> | |
29 <install version="1.0"> | |
30 <actions> | |
31 <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> | |
32 <action type="shell_command">make all</action> | |
33 <action type="make_directory">$INSTALL_DIR/bin</action> | |
34 <action type="move_directory_files"> | |
35 <source_directory>bin</source_directory> | |
36 <destination_directory>$INSTALL_DIR/bin</destination_directory> | |
37 </action> | |
38 <action type="set_environment"> | |
39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
40 </action> | |
41 </actions> | |
42 </install> | |
43 <readme> | |
44 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required | |
45 </readme> | |
46 </package> | |
47 <package name="contra" version="2.0.4"> | |
48 <install version="1.0"> | |
49 <actions> | |
50 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action> | |
51 <action type="shell_command">rm -rf bedtools_installation_guide.txt</action> | |
52 <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action> | |
53 <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action> | |
54 <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action> | |
55 <action type="make_directory">$INSTALL_DIR/bin</action> | |
56 <action type="make_directory">$INSTALL_DIR/bin/scripts</action> | |
57 <action type="move_file"> | |
58 <source>contra.py</source> | |
59 <destination>$INSTALL_DIR/bin</destination> | |
60 </action> | |
61 <action type="move_file"> | |
62 <source>baseline.py</source> | |
63 <destination>$INSTALL_DIR/bin</destination> | |
64 </action> | |
65 <action type="move_directory_files"> | |
66 <source_directory>scripts</source_directory> | |
67 <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory> | |
68 </action> | |
69 <action type="set_environment"> | |
70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
71 </action> | |
72 </actions> | |
73 </install> | |
74 <readme> | |
75 Contra requires Samtools, Bedtools, Python and R | |
76 </readme> | |
77 </package> | |
78 </tool_dependency> | |
79 | |
80 |