Mercurial > repos > yhoogstrate > edger_with_design_matrix

diff tool_dependencies.xml @ 79:c86f1f86b3c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yhoogstrate
date Thu, 13 Nov 2014 10:30:43 -0500
parents 398963a4827a
children c5bd139cd3e8
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Sep 30 11:29:52 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 13 10:30:43 2014 -0500
@@ -1,38 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	
-	<!-- the following repo does NOT work out of the box:
-	<package name="package_r3_withx" version="3.0.1">
-		<repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-	</package>
-	-->
-	
-	<!-- the following repo does NOT even install due to gfortran shared libs:
-	<package name="R" version="3.1.0">
-		<repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-	</package>
-	-->
-	
 	<package name="R" version="3.0.3">
-		<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+		<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /><!-- toolshed="http://testtoolshed.g2.bx.psu.edu/" -->
 	</package>
 	
 	<package name="biocLite_edgeR_limma" version="latest">
 		<install version="1.0"> 
 			<actions>
 				<action type="set_environment_for_install">
-					<!-- the following repo does NOT work out of the box:
-					<repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-						<package name="package_r3_withx" version="3.0.1" />
-					</repository>
-					-->
-					<!-- the following repo does NOT even install due to gfortran shared libs:
-					<repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-						<package name="R" version="3.1.0" />
-					</repository>
-					-->
-					
-					<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+					<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"><!-- toolshed="http://testtoolshed.g2.bx.psu.edu/" -->
 						<package name="R" version="3.0.3" />
 					</repository>
 					
@@ -54,6 +30,23 @@
 	
 	<!-- instead of using "convert", make use of "gm convert" -->
 	<package name="graphicsmagick" version="1.3.18">
-		<repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+		<repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /><!-- toolshed="http://testtoolshed.g2.bx.psu.edu/" -->
+	</package>
+	
+	<package name="design_matrix_creator" version="1.0.0">
+		<install version="1.0">
+			<actions>
+				<action type="move_file">
+					<source>$REPOSITORY_INSTALL_DIR/design_matrix_creator</source>
+					<destination>$INSTALL_DIR/bin/</destination>
+				</action>
+				<action type="chmod">
+					<file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
+				</action>
+				<action type="set_environment">
+					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
 	</package>
 </tool_dependency>