Mercurial > repos > shians > package_shrnaseq_1_2_1

changeset 14:282c4d135b86

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- Alternate github links
author shian_su <registertonysu@gmail.com>
date Thu, 20 Nov 2014 15:46:39 +1100
parents b4516e2c7625
children d9a59a6fe227
files tool_dependencies.xml
diffstat 1 files changed, 7 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Nov 20 15:40:19 2014 +1100
+++ b/tool_dependencies.xml	Thu Nov 20 15:46:39 2014 +1100
@@ -11,15 +11,22 @@
                         <package name="R_3_0_1" version="3.0.1" />
                     </repository>
                 </action>
+                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</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/raw/master/dependencies/limma_3.22.1.tar.gz</action>
                 <action type="download_file">https://github.com/Shians/diffexp/raw/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/shrnaseq/ &amp;&amp;
+                    Rscript -e "install.packages(c('BiocGenerics_0.6.0.tar.gz', repos=NULL, dependencies=FALSE)"
+                    <!--
                     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>