Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

annotate tool_dependencies.xml @ 6:5a242f289347 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Merge
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents b2eb07000039
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
1 <?xml version="1.0"?>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
2 <tool_dependency>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
3 <package name="R" version="3.1.2">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
4 <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
5 owner="iuc" prior_installation_required="True"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
6 toolshed="http://toolshed.g2.bx.psu.edu" />
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
7 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
8 <package name="readline" version="6.2">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
9 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
10 owner="iuc" prior_installation_required="True"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
11 toolshed="http://toolshed.g2.bx.psu.edu" />
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
12 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
13 <package name="rpy2" version="2.3.10">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
14 <install version="1.0">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
15 <actions>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
16 <action type="download_by_url">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
17 https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.10.tar.gz
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
18 </action>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
19 <action type="set_environment_for_install">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
20 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
21 owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
22 <package name="readline" version="6.2" />
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
23 </repository>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
24 <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
25 owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
26 <package name="R" version="3.1.2" />
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
27 </repository>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
28 </action>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
29 <action type="shell_command">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
31 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
32 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
33 python setup.py build --r-home $R_HOME --r-home-lib $R_HOME/lib install --install-lib $INSTALL_DIR/lib/python
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
34 </action>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
35 <action type="set_environment">
2
b2eb07000039 Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 0
diff changeset
36 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
b2eb07000039 Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 0
diff changeset
37 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[READLINE_LIB_PATH]</environment_variable>
b2eb07000039 Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 0
diff changeset
38 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[RHOME]/lib</environment_variable>
b2eb07000039 Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 0
diff changeset
39 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[R_ROOT_DIR]/lib</environment_variable>
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
40 </action>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
41 </actions>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
42 </install>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
43 <readme>rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
44 a proposed high-level interface, including wrappers to graphical libraries,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
45 as well as R-like structures and functions.
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
46
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
47 http://rpy.sourceforge.net/rpy2.html
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
48 </readme>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
49 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
50 <package name="riboseqr_wrapper_deps" version="0.4.0">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
51 <install version="1.0">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
52 <actions>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
53 <action type="setup_r_environment">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
54 <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
55 owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
56 <package name="R" version="3.1.2" />
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
57 </repository>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
58 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
59 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/BiocGenerics_0.12.1.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
60 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
61 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
62 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/S4Vectors_0.4.0.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
63 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
64 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
65 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/IRanges_2.0.1.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
66 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
67 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
68 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/GenomeInfoDb_1.2.5.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
69 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
70 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
71 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/XVector_0.6.0.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
72 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
73 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
74 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/GenomicRanges_1.18.4.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
75 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
76 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
77 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/abind_1.4-3.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
78 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
79 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
80 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/baySeq_2.0.50.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
81 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
82 <package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
83 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/riboSeqR_1.0.5.tar.gz?raw=true
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
84 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
85 </action>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
86 </actions>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
87 </install>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
88 <readme>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
89 Dependency installation for riboseqr_wrapper
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
90 </readme>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
91 </package>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
92 </tool_dependency>