Mercurial > repos > jjohnson > package_bioc_geneplotter_1_36_0

changeset 0:20aa0e1b2c21 draft default tip

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Imported from capsule None
author jjohnson
date Mon, 22 Sep 2014 11:54:37 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 48 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Sep 22 11:54:37 2014 -0400
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="libxml2" version="2.9.1">
+      <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R" version="2.15.0">
+      <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioc_geneplotter" version="1.36.0">
+      <install version="1.0">
+          <actions>
+              <action type="set_environment_for_install">
+                  <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                      <package name="libxml2" version="2.9.1" />
+                    </repository>
+                </action>
+                <action type="set_environment_for_install">
+                  <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                      <package name="R" version="2.15.0" />
+                    </repository>
+                </action>
+                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/BiocGenerics_0.4.0.tar.gz</action>
+                <action type="download_file">http://cran.fhcrc.org/src/contrib/DBI_0.3.0.tar.gz</action>
+                <action type="download_file">http://cran.fhcrc.org/src/contrib/xtable_1.7-4.tar.gz</action>
+                <action type="download_file">http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz</action>
+                <action type="download_file">http://cran.fhcrc.org/src/contrib/RSQLite_0.11.4.tar.gz</action>
+                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/IRanges_1.16.6.tar.gz</action>
+                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/Biobase_2.18.0.tar.gz</action>
+                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/annotate_1.36.0.tar.gz</action>
+                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/AnnotationDbi_1.20.7.tar.gz</action>
+                <action type="download_file">http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz</action>
+                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/geneplotter_1.36.0.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/geneplotter/</action>
+                <action type="shell_command">
+                    export PATH=$PATH:$R_HOME/bin &amp;&amp;
+                    export R_LIBS=$INSTALL_DIR/geneplotter/ &amp;&amp;
+                    Rscript -e "install.packages(c('BiocGenerics_0.4.0.tar.gz','DBI_0.3.0.tar.gz','xtable_1.7-4.tar.gz','XML_3.98-1.1.tar.gz','RColorBrewer_1.0-5.tar.gz','RSQLite_0.11.4.tar.gz','IRanges_1.16.6.tar.gz','Biobase_2.18.0.tar.gz','AnnotationDbi_1.20.7.tar.gz','annotate_1.36.0.tar.gz','geneplotter_1.36.0.tar.gz'),lib='$INSTALL_DIR/geneplotter/', repos=NULL, dependencies=FALSE)"
+                </action>
+                <action type="set_environment">
+                  <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/geneplotter/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Install the geneplotter package (version 1.36.0) from BioConductor (version 2.11)
+        </readme>
+    </package>
+</tool_dependency>