Mercurial > repos > iuc > package_deseq2_1_0_17

changeset 1:0e80b1827773 draft

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add rjson as dependency
author iuc
date Tue, 24 Sep 2013 10:34:47 -0400
parents da4a76f019e6
children f1e274c5dafe
files tool_dependencies.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Sep 23 14:51:49 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 24 10:34:47 2013 -0400
@@ -29,12 +29,15 @@
                 <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/genefilter_1.42.0.tar.gz</action>
                 <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RColorBrewer_1.0-5.tar.gz</action>
                 <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DESeq2_1.0.18.tar.gz</action>
+                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/rjson_0.2.13.tar.gz</action>
+                <!--<action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/biomaRt_2.16.0.tar.gz</action>-->
+
 
                 <action type="make_directory">$INSTALL_DIR/deseq2/</action>
                 <action type="shell_command">
                     export PATH=$PATH:$R_HOME/bin &amp;&amp; 
                     export R_LIBS=$INSTALL_DIR/deseq2/ &amp;&amp; 
-                    Rscript -e "install.packages(c('BiocGenerics_0.6.0.tar.gz','IRanges_1.18.2.tar.gz','GenomicRanges_1.12.4.tar.gz','Rcpp_0.10.4.tar.gz','RcppArmadillo_0.3.900.0.tar.gz','locfit_1.5-9.1.tar.gz','Biobase_2.20.1.tar.gz','DBI_0.2-7.tar.gz','RSQLite_0.11.4.tar.gz','AnnotationDbi_1.22.6.tar.gz','xtable_1.7-1.tar.gz','XML_3.98-1.1.tar.gz','annotate_1.38.0.tar.gz','genefilter_1.42.0.tar.gz','RColorBrewer_1.0-5.tar.gz','DESeq2_1.0.18.tar.gz'),lib='$INSTALL_DIR/deseq2/', repos=NULL, dependencies=FALSE)"
+                    Rscript -e "install.packages(c('BiocGenerics_0.6.0.tar.gz','IRanges_1.18.2.tar.gz','GenomicRanges_1.12.4.tar.gz','Rcpp_0.10.4.tar.gz','RcppArmadillo_0.3.900.0.tar.gz','locfit_1.5-9.1.tar.gz','Biobase_2.20.1.tar.gz','DBI_0.2-7.tar.gz','RSQLite_0.11.4.tar.gz','AnnotationDbi_1.22.6.tar.gz','xtable_1.7-1.tar.gz','XML_3.98-1.1.tar.gz','annotate_1.38.0.tar.gz','genefilter_1.42.0.tar.gz','RColorBrewer_1.0-5.tar.gz','DESeq2_1.0.18.tar.gz', 'rjson_0.2.13.tar.gz'),lib='$INSTALL_DIR/deseq2/', repos=NULL, dependencies=FALSE)"
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>