Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 83:b2738b4d7c8c draft

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author yhoogstrate
date Wed, 19 Nov 2014 08:55:40 -0500
parents 8c4f96e8ebf1
children ddcc677fb13d
files README.md README.rst edgeR_Concatenate_Expression_Matrices.xml edgeR_Design_from_Expression_Matrix.xml edgeR_Differential_Gene_Expression.xml edger_with_design_matrix.tar.xz tool_dependencies.xml
diffstat 7 files changed, 86 insertions(+), 73 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Thu Nov 13 16:10:47 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-EdgeR wrapper for Galaxy
-========================
-
-<http://www.bioconductor.org/packages/release/bioc/html/edgeR.html>
-
-Implementation of EdgeR supporting quite advanced experimental
-designs.
-
-Development
------------
-
-* Repository-Maintainer: Youri Hoogstrate
-
-* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools>
-
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus
-Medical Center (Rotterdam, Netherlands) on behalf of the Translational
-Research IT (TraIT) project:
-
-<http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch>
-
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-
-<http://toolshed.dtls.nl/>
-
-License
--------
-
-**R**:
-
-<http://www.r-project.org/COPYING>
-
-GPL (>=2)
-
-**BioConductor**:
-
-<http://www.bioconductor.org/about/>
-
-Artistic License 2.0
-
-**EdgeR**:
-
-GPL (>=2)
-
-**This wrapper**:
-
-    Copyright (C) 2013-2014  Youri Hoogstrate
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Nov 19 08:55:40 2014 -0500
@@ -0,0 +1,60 @@
+EdgeR wrapper for Galaxy
+========================
+
+<http://www.bioconductor.org/packages/release/bioc/html/edgeR.html>
+
+Implementation of EdgeR supporting quite advanced experimental
+designs.
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools>
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+<http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch>
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+
+<http://toolshed.dtls.nl/>
+
+License
+-------
+
+**R**:
+
+<http://www.r-project.org/COPYING>
+
+GPL (>=2)
+
+**BioConductor**:
+
+<http://www.bioconductor.org/about/>
+
+Artistic License 2.0
+
+**EdgeR**:
+
+GPL (>=2)
+
+**This wrapper**:
+
+    Copyright (C) 2013-2014  Youri Hoogstrate
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
--- a/edgeR_Concatenate_Expression_Matrices.xml	Thu Nov 13 16:10:47 2014 -0500
+++ b/edgeR_Concatenate_Expression_Matrices.xml	Wed Nov 19 08:55:40 2014 -0500
@@ -145,12 +145,16 @@
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
 Research IT (TraIT) project:
+
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
 More tools by the Translational Research IT (TraIT) project can be found
 in the following toolsheds:
-- http://toolshed.dtls.nl/
-- http://toolshed.g2.bx.psu.edu
-- http://testtoolshed.g2.bx.psu.edu/
+
+http://toolshed.dtls.nl/
+
+http://toolshed.g2.bx.psu.edu
+
+http://testtoolshed.g2.bx.psu.edu/
 	</help>
 </tool>
--- a/edgeR_Design_from_Expression_Matrix.xml	Thu Nov 13 16:10:47 2014 -0500
+++ b/edgeR_Design_from_Expression_Matrix.xml	Wed Nov 19 08:55:40 2014 -0500
@@ -112,12 +112,16 @@
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
 Research IT (TraIT) project:
+
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
 More tools by the Translational Research IT (TraIT) project can be found
 in the following toolsheds:
-- http://toolshed.dtls.nl/
-- http://toolshed.g2.bx.psu.edu
-- http://testtoolshed.g2.bx.psu.edu/
+
+http://toolshed.dtls.nl/
+
+http://toolshed.g2.bx.psu.edu
+
+http://testtoolshed.g2.bx.psu.edu/
 	</help>
 </tool>
--- a/edgeR_Differential_Gene_Expression.xml	Thu Nov 13 16:10:47 2014 -0500
+++ b/edgeR_Differential_Gene_Expression.xml	Wed Nov 19 08:55:40 2014 -0500
@@ -608,13 +608,17 @@
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
 Research IT (TraIT) project:
+
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
 More tools by the Translational Research IT (TraIT) project can be found
 in the following toolsheds:
-- http://toolshed.dtls.nl/
-- http://toolshed.g2.bx.psu.edu
-- http://testtoolshed.g2.bx.psu.edu/
+
+http://toolshed.dtls.nl/
+
+http://toolshed.g2.bx.psu.edu
+
+http://testtoolshed.g2.bx.psu.edu/
 
 I would like to thank Hina Riaz - Naz Khan for her helpful contribution.
 	</help>
Binary file edger_with_design_matrix.tar.xz has changed
--- a/tool_dependencies.xml	Thu Nov 13 16:10:47 2014 -0500
+++ b/tool_dependencies.xml	Wed Nov 19 08:55:40 2014 -0500
@@ -1,14 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	<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" />
 	</package>
 	
 	<package name="biocLite_edgeR_limma" version="latest">
 		<install version="1.0"> 
 			<actions>
 				<action type="set_environment_for_install">
-					<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">
 						<package name="R" version="3.0.3" />
 					</repository>
 					
@@ -30,7 +30,7 @@
 	
 	<!-- 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="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
 	
 	<package name="design_matrix_creator" version="1.0.0">
@@ -44,7 +44,8 @@
 					<file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
 				</action>
 				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
 				</action>
 			</actions>
 		</install>