Mercurial > repos > nilesh > rseqc

changeset 7:e676f86496e7

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Deleted selected files
author nilesh
date Mon, 08 Jul 2013 22:10:38 -0400
parents e6e8ce41f13f
children e1c6951bd6fc
files tool_dependencies.xml
diffstat 1 files changed, 0 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Jul 08 22:06:12 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="R" version="2.15.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
-                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
-                <action type="shell_command">make</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.</readme>
-    </package>
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
-    </package>
-    <package name="rseqc" version="2.3.7">
-        <install version = "1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
-                <action type="shell_command">python setup.py install</action>
-                <action action="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR/lib/rseqc</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        	RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
-        </readme>
-    </package>
-    
-</tool_dependency>