Mercurial > repos > bgruening > package_deseq2_1_0_17

changeset 4:eab36a9a70b1 draft

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Uploaded
author bgruening
date Fri, 02 Aug 2013 13:15:42 -0400
parents 6d4dbaa47b83
children 3e3d1a50a347
files tool_dependencies.xml
diffstat 1 files changed, 19 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 02 07:33:28 2013 -0400
+++ b/tool_dependencies.xml	Fri Aug 02 13:15:42 2013 -0400
@@ -1,38 +1,40 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="4dba1ce455da" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bae5c9880b71" name="package_r_3_0_1" 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="set_environment_for_install">
-                    <repository changeset_revision="4dba1ce455da" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <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>
 
-<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz</action>
-<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/IRanges_1.18.2.tar.gz</action>
-<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/annotate_1.38.0.tar.gz</action>
-<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/GenomicRanges_1.12.4.tar.gz</action>
-<action type="download_file">http://cran.fhcrc.org/src/contrib/Rcpp_0.10.4.tar.gz</action>
-<action type="download_file">http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.3.900.0.tar.gz</action>
-<action type="download_file">http://cran.fhcrc.org/src/contrib/locfit_1.5-9.1.tar.gz</action>
-<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/genefilter_1.42.0.tar.gz</action>
-<action type="download_file">http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz</action>
-<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/DESeq2_1.0.18.tar.gz</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="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","annotate_1.38.0.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","genefilter_1.42.0.tar.gz","RColorBrewer_1.0-5.tar.gz","DESeq2_1.0.18.tar.gz",),lib="$INSTALL_DIR/deseq2/",  repos=NULL, dependencies=FALSE)"
-
+                    Rscript -e "install.packages(c('BiocGenerics_0.6.0.tar.gz','IRanges_1.18.2.tar.gz','GenomicRanges_1.12.4.tar.gz','Rcpp_0.10.4.tar.gz','RcppArmadillo_0.3.900.0.tar.gz','locfit_1.5-9.1.tar.gz','Biobase_2.20.1.tar.gz','DBI_0.2-7.tar.gz','RSQLite_0.11.4.tar.gz','AnnotationDbi_1.22.6.tar.gz','xtable_1.7-1.tar.gz','XML_3.98-1.1.tar.gz','annotate_1.38.0.tar.gz','genefilter_1.42.0.tar.gz','RColorBrewer_1.0-5.tar.gz','DESeq2_1.0.18.tar.gz'),lib='$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>