annotate tool_dependencies.xml @ 25:7cac660d1c0a

Uploaded
author nilesh
date Thu, 11 Jul 2013 12:25:38 -0400
parents 6f150036a010
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
6f150036a010 Uploaded
nilesh
parents:
diff changeset
1 <?xml version="1.0"?>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
2 <tool_dependency>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
3 <package name="R" version="2.15.1">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
4 <install version="1.0">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
5 <actions>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
6 <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
7 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
8 <action type="shell_command">make</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
9 <action type="set_environment">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
10 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
11 </action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
12 </actions>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
13 </install>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
14 <readme>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
15 You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
6f150036a010 Uploaded
nilesh
parents:
diff changeset
16 </readme>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
17 </package>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
18 <package name="samtools" version="0.1.18">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
19 <install version="1.0">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
20 <actions>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
21 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
22 <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
23 <action type="shell_command">make</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
24 <action type="move_file">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
25 <source>samtools</source>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
26 <destination>$INSTALL_DIR/bin</destination>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
27 </action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
28 <action type="move_file">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
29 <source>misc/maq2sam-long</source>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
30 <destination>$INSTALL_DIR/bin</destination>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
31 </action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
32 <action type="set_environment">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
33 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
34 </action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
35 </actions>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
36 </install>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
37 <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
38 </package>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
39 <package name="rseqc" version="2.3.7">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
40 <install version = "1.0">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
41 <actions>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
42 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
43 <action type="shell_command">python setup.py install --root</action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
44 <action action="move_directory_files">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
45 <source_directory>.</source_directory>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
46 <destination_directory>$INSTALL_DIR/lib/rseqc</destination_directory>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
47 </action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
48 <action type="set_environment">
6f150036a010 Uploaded
nilesh
parents:
diff changeset
49 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
50 </action>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
51 </actions>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
52 </install>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
53 <readme>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
54 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
6f150036a010 Uploaded
nilesh
parents:
diff changeset
55 </readme>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
56 </package>
6f150036a010 Uploaded
nilesh
parents:
diff changeset
57
6f150036a010 Uploaded
nilesh
parents:
diff changeset
58 </tool_dependency>