Mercurial > repos > biomonika > test_dependency

changeset 12:0f7ae03642e3

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d4
author biomonika <biomonika@psu.edu>
date Mon, 25 Aug 2014 14:44:33 -0400
parents 01811c70635c
children 0659a0a8e6fd
files tool_dependencies.xml
diffstat 1 files changed, 7 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Aug 25 14:35:49 2014 -0400
+++ b/tool_dependencies.xml	Mon Aug 25 14:44:33 2014 -0400
@@ -3,31 +3,20 @@
         <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
 
-    <package name="samtools" version="0.1.18">
+    <package name="samtools" version="0.1.19">
         <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="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
                 <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile</action>
                 <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>libbam.a</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-               <action type="move_file">
-                    <source>bam.h</source>
-                    <destination>$INSTALL_DIR/bin</destination>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
-    </package>
\ No newline at end of file
+    </package>
+</tool_dependency>
\ No newline at end of file