Mercurial > repos > iuc > package_homer_4_2

changeset 0:f59c0d41c9d9 draft

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Uploaded
author iuc
date Fri, 21 Mar 2014 08:14:44 -0400
parents
children e38be1da9ed3
files tool_dependencies.xml
diffstat 1 files changed, 46 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Mar 21 08:14:44 2014 -0400
@@ -0,0 +1,46 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ghostscript" version="9.07">
+        <repository changeset_revision="6261034b0d94" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="weblogo" version="2.8.2">
+        <repository changeset_revision="18d9e18fa00b" name="package_weblogo_2_8_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="blat" version="35x1">
+        <repository changeset_revision="7172d70a3c31" name="package_blat_35x1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="homer" version="4.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://biowhat.ucsd.edu/homer/homer.v4.2.zip</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="6261034b0d94" name="package_ghostscript_9_07" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="ghostscript" version="9.07" />
+                    </repository>
+                    <repository changeset_revision="18d9e18fa00b" name="package_weblogo_2_8_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="weblogo" version="2.8.2" />
+                    </repository>
+                    <repository changeset_revision="7172d70a3c31" name="package_blat_35x1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="blat" version="35x1" />
+                    </repository>
+                </action>
+
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/homer</destination_directory>
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PATH">$INSTALL_DIR/homer/bin</environment_variable>
+                    <environment_variable action="append_to" name="PATH">$ENV[WEBLOGO_PATH]</environment_variable>
+                    <environment_variable action="append_to" name="PATH">$ENV[GHOSTSCRIPT_PATH]</environment_variable>
+                    <environment_variable action="append_to" name="PATH">$ENV[BLAT_PATH]</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Installing HOMER requires a perl environment. http://biowhat.ucsd.edu/homer/</readme>
+    </package>
+</tool_dependency>