Mercurial > repos > rnateam > package_segemehl_0_1_6

changeset 0:7078b80ffc12 draft default tip

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author rnateam
date Tue, 05 Nov 2013 09:00:17 -0500
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 27 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Nov 05 09:00:17 2013 -0500
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="segemehl" version="0.1.6">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url" target_filename="segemehl_0_1_6_1.tar.gz">http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_1_6.tar.gz</action>
+                <action type="change_directory">segemehl</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>segemehl.x</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Short read mapping with gaps.
+            To compile segemehl a C-compiler is needed, usually GCC.
+            http://www.bioinf.uni-leipzig.de/Software/segemehl/
+            
+            Please note that segemehl loads the whole index and genome files into memory.
+            Segemehl's index is around 45GB in size, so the memory usage of that tool is huge.
+        </readme>
+    </package>
+</tool_dependency>