Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 0:acb56603b268 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
author yhoogstrate
date Mon, 31 Aug 2015 11:00:02 -0400
parents
children a4a4c88783ea
files tool_dependencies.xml
diffstat 1 files changed, 60 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 31 11:00:02 2015 -0400
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="R" version="3.0.3">
+		<repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="a8438aa1207c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+						<package name="R" version="3.0.3" />
+					</repository>
+					
+				</action>
+				<action type="make_directory">$INSTALL_DIR</action>
+				<action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
+				<action type="shell_command">echo "installme=c('edgeR','limma')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+				<action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
+				<action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+				<action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+				<action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+				<action type="shell_command">export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+			</actions>
+		</install>
+		<readme>
+			Installs the latest bioc packages: edgeR &amp; Limma
+	   </readme>
+	</package>
+	
+	<package name="design_matrix_creator" version="1.0.0">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action>
+				<action type="chmod">
+					<file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
+				</action>
+				<action type="set_environment">
+					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+				</action>
+			</actions>
+		</install>
+	</package>
+	
+	<package name="edger_dge_table_to_bedgraph" version="1.0.0">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action>
+				<action type="chmod">
+					<file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file>
+				</action>
+				<action type="set_environment">
+					<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>
+	</package>
+</tool_dependency>