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diff tool_dependencies.xml @ 5:3bd1087db05e draft

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Add dependecies for bowtie, blat, and faToTwoBit
author Jim Johnson <jj@umn.edu>
date Fri, 04 Jan 2013 15:01:19 -0600
parents 679a5c7b1294
children 1ea6445491d4
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jan 04 13:29:03 2013 -0600
+++ b/tool_dependencies.xml	Fri Jan 04 15:01:19 2013 -0600
@@ -18,4 +18,77 @@
         </readme>
     </package>
 
+    <package name="bowtie" version="0.12.7">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>bowtie</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie-build</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie-inspect</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 Bowtie requires libpthread to be present on your system.
+        </readme>
+    </package>
+
+    <package name="blat" version="34x10">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
+                <action type="shell_command">chmod 755 blat</action>
+                <action type="move_file">
+                    <source>blat</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>
+This only handles blat for a non-commercial linux system.
+
+Please note that the Blat source and executables are freely available for
+academic, nonprofit and personal use. Commercial licensing information is
+available on the Kent Informatics website (http://www.kentinformatics.com/).
+        </readme>
+    </package>
+
+    <package name="fatotwobit" version="34x10">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
+                <action type="shell_command">chmod 755 faToTwoBit</action>
+                <action type="move_file">
+                    <source>faToTwoBit</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>
+This only handles faToTwoBit for a non-commercial linux system.
+
+Please note that the source and executables are freely available for
+academic, nonprofit and personal use. Commercial licensing information is
+available on the Kent Informatics website (http://www.kentinformatics.com/).
+        </readme>
+    </package>
+
 </tool_dependency>