Mercurial > repos > bgruening > package_deseq2_1_0_17

changeset 5:3e3d1a50a347 draft

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Uploaded
author bgruening
date Mon, 16 Sep 2013 10:09:20 -0400
parents eab36a9a70b1
children ec26508b1a2a
files tool_dependencies.xml
diffstat 1 files changed, 26 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 02 13:15:42 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 16 10:09:20 2013 -0400
@@ -7,44 +7,42 @@
     <package name="deseq2" version="1.0.17">
         <install version="1.0">
             <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="bae5c9880b71" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+
+                <action type="setup_r_environment">
+
+                    <repository name="package_r_3_0_1" owner="bgruening">
                         <package name="R_3_0_1" version="3.0.1" />
                     </repository>
+
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/IRanges_1.18.2.tar.gz</r_package>
+
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/GenomicRanges_1.12.4.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Rcpp_0.10.4.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RcppArmadillo_0.3.900.0.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Biobase_2.20.1.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DBI_0.2-7.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RSQLite_0.11.4.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/AnnotationDbi_1.22.6.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/xtable_1.7-1.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/XML_3.98-1.1.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/annotate_1.38.0.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/genefilter_1.42.0.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RColorBrewer_1.0-5.tar.gz</r_package>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DESeq2_1.0.18.tar.gz</r_package>
+
                 </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/bgruening/download_store/raw/master/DESeq2-1_0_18/IRanges_1.18.2.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/GenomicRanges_1.12.4.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Rcpp_0.10.4.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RcppArmadillo_0.3.900.0.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Biobase_2.20.1.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DBI_0.2-7.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RSQLite_0.11.4.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/AnnotationDbi_1.22.6.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/xtable_1.7-1.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/XML_3.98-1.1.tar.gz</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/annotate_1.38.0.tar.gz</action>
-                <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="set_environment">
+                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR</environment_variable>
+                </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='$INSTALL_DIR/deseq2/', repos=NULL, dependencies=FALSE)"
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
-                </action>
             </actions>
         </install>
         <readme>
         Differential gene expression analysis based on the negative binomial distribution.
         http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
-        Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
         </readme>
     </package>
 </tool_dependency>