Mercurial > repos > paulgordon > atlas2

changeset 0:59d3e3484f16 draft

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Uploaded
author paulgordon
date Mon, 11 Feb 2013 15:40:56 -0500
parents
children da1dba1da40a
files tool_dependencies.xml
diffstat 1 files changed, 36 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Feb 11 15:40:56 2013 -0500
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="atlas2" version="1.4.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/atlas2/files/Atlas2_v1.4.1.zip/download</action>
+                <action type="move_directory_files">
+                    <source_directory>Atlas-Indel2</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Atlas2 requires Ruby 1.9.1+. Installation requires the Zip archiver software.
+        </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>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
+    </package>
+</tool_dependency>