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changeset 36:0fa6327f9281

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Uploaded
author bgruening
date Sun, 30 Jun 2013 15:42:01 -0400
parents 7d57dba74532
children 82f2cce7d379
files tool_dependencies.xml
diffstat 1 files changed, 21 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Jun 06 02:34:41 2013 -0400
+++ b/tool_dependencies.xml	Sun Jun 30 15:42:01 2013 -0400
@@ -1,18 +1,31 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="fastqc_dist_0_10_1" version="0.10.1">
+    <package name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="4e9dce1105cd" name="precommit_test" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+
+
+    <package name="deseq2" version="1.0.17">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>../FastQC</source_directory>
-                    <destination_directory>$INSTALL_DIR/fastqc_dist</destination_directory>
-                </action>                
-                <action type="shell_command">chmod ugo+x $INSTALL_DIR/fastqc_dist/fastqc</action>
+                <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.0.17.tar.gz</action>
+
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="4e9dce1105cd" name="precommit_test" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="R_3_0_1" version="3.0.1" />
+                    </repository>
+                </action>
+
+                <action type="make_directory">$INSTALL_DIR/deseq2/</action>
+                <action type="shell_command">
+                    Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages('DESeq2', lib='$INSTALL_DIR/deseq2/', repos='http://cran.us.r-project.org')"
+                </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/fastqc_dist</environment_variable>
+                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
                 </action>
             </actions>
         </install>
+        <readme>DESeq2</readme>
     </package>
 </tool_dependency>