Mercurial > repos > fcaramia > methylation_analysis_bismark

changeset 15:d2ba233899b0 draft default tip

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Uploaded
author fcaramia
date Mon, 17 Jun 2013 21:50:56 -0400
parents cdb7231da7f2
children
files tool_dependencies.xml
diffstat 1 files changed, 24 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Jun 17 21:44:43 2013 -0400
+++ b/tool_dependencies.xml	Mon Jun 17 21:50:56 2013 -0400
@@ -3,6 +3,30 @@
     <set_environment version="1.0">
         <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
+    <package name="samtools" version="0.1.18">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
+                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$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="bowtie2" version="2.0.0-beta7">
         <install version="1.0">
             <actions>