Mercurial > repos > bgruening > package_deseq2_1_0_17

changeset 7:b7272a300fce draft

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Uploaded
author bgruening
date Tue, 22 Oct 2013 16:13:38 -0400
parents ec26508b1a2a
children e748fa5bdbab
files tool_dependencies.xml
diffstat 1 files changed, 22 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Sep 30 12:51:19 2013 -0400
+++ b/tool_dependencies.xml	Tue Oct 22 16:13:38 2013 -0400
@@ -1,46 +1,36 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_r_3_0_1" owner="iuc" prior_installation_required="True" />
     </package>
 
     <package name="deseq2" version="1.0.17">
         <install version="1.0">
             <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                <action type="setup_r_environment">
+
+                    <repository changeset_revision="bae5c9880b71" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="R_3_0_1" version="3.0.1" />
                     </repository>
-                </action>
+
+                    <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>
 
-                <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="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', '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>
+                    <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>
+                    <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/rjson_0.2.13.tar.gz<r_package>
                 </action>
             </actions>
         </install>