Mercurial > repos > shians > package_shrnaseq_1_2_1

changeset 0:d2ef31a1ed1b

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- Initial commit
author shian_su <registertonysu@gmail.com>
date Thu, 20 Nov 2014 14:47:31 +1100
parents
children d59334f0cfe4
files tool_dependencies.xml
diffstat 1 files changed, 36 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Nov 20 14:47:31 2014 +1100
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R_3_1_1" version="3.1.1">
+        <repository name="package_r_3_1_1" owner="fubar" prior_installation_required="True" />
+    </package>
+    
+    <package name="shrnaseq" version="1.2.1">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository name="package_r_3_1_1" owner="fubar" />
+                        <package name="R_3_1_1" version="3.1.1" />
+                    </repository>
+                </action>
+                
+                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/locfit_1.5-9.1.tar.gz</action>
+                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/statmod_1.4.20.tar.gz</action>
+                <action type="download_file">https://github.com/Shians/diffexp/commits/master/dependencies/limma_3.22.1.tar.gz</action>
+                <action type="download_file">https://github.com/Shians/diffexp/commits/master/dependencies/edgeR_3.8.3.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/shrnaseq/</action>
+                <action type="shell_command">
+                    export PATH=$PATH:$R_HOME/bin &amp;&amp;
+                    export R_LIBS=$INSTALL_DIR/deseq2/ &amp;&amp;
+                    Rscript -e "install.packages(c('locfit_1.5-9.1.tar.gz', 'statmod_1.4.20.tar.gz', 'limma_3.22.1.tar.gz', 'edgeR_3.8.3.tar.gz'),lib='$INSTALL_DIR/shrnaseq/', repos=NULL, dependencies=FALSE)"
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/shrnaseq/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            shrnaseq analysis using edgeR bioConductor package.
+            http://bioconductor.org/packages/release/bioc/html/edgeR.html
+        </readme>
+    </package>
+</tool_dependency>