Mercurial > repos > fcaramia > contra

annotate tool_dependencies.xml @ 24:6bcf47cc272a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author fcaramia
date Mon, 19 May 2014 20:00:44 -0400
parents 2770f49cb0dc
children c361b3fb806e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
1 <?xml version="1.0"?>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
2 <tool_dependency>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
3 <package name="samtools" version="0.1.18">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
4 <install version="1.0">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
5 <actions>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
6 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
7 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
8 <action type="shell_command">make</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
9 <action type="move_file">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
10 <source>samtools</source>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
11 <destination>$INSTALL_DIR/bin</destination>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
12 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
13 <action type="move_file">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
14 <source>misc/maq2sam-long</source>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
15 <destination>$INSTALL_DIR/bin</destination>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
16 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
17 <action type="set_environment">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
19 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
20 </actions>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
21 </install>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
22 <readme>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
23 Compiling SAMtools requires the ncurses and zlib development libraries.
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
24 </readme>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
25 </package>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
26
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
27
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
28 <package name="bedtools" version="2.17.0">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
29 <install version="1.0">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
30 <actions>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
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>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
32 <action type="shell_command">make all</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
33 <action type="make_directory">$INSTALL_DIR/bin</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
34 <action type="move_directory_files">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
35 <source_directory>bin</source_directory>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
36 <destination_directory>$INSTALL_DIR/bin</destination_directory>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
37 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
38 <action type="set_environment">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
40 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
41 </actions>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
42 </install>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
43 <readme>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
44 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
45 </readme>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
46 </package>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
47 <package name="contra" version="2.0.4">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
48 <install version="1.0">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
49 <actions>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
50 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
51 <action type="shell_command">rm -rf bedtools_installation_guide.txt</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
52 <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
53 <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
54 <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
55 <action type="make_directory">$INSTALL_DIR/bin</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
56 <action type="make_directory">$INSTALL_DIR/bin/scripts</action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
57 <action type="move_file">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
58 <source>contra.py</source>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
59 <destination>$INSTALL_DIR/bin</destination>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
60 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
61 <action type="move_file">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
62 <source>baseline.py</source>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
63 <destination>$INSTALL_DIR/bin</destination>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
64 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
65 <action type="move_directory_files">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
66 <source_directory>scripts</source_directory>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
67 <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
68 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
69 <action type="set_environment">
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
71 </action>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
72 </actions>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
73 </install>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
74 <readme>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
75 Contra requires Samtools, Bedtools, Python and R
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
76 </readme>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
77 </package>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
78 </tool_dependency>
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
79
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
80