Mercurial > repos > iuc > package_deseq2_1_0_17

changeset 0:da4a76f019e6 draft

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initial Upload
author iuc
date Mon, 23 Sep 2013 14:51:49 -0400
parents
children 0e80b1827773
files tool_dependencies.xml
diffstat 1 files changed, 50 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Sep 23 14:51:49 2013 -0400
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="d2ebbabb4523" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.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="d2ebbabb4523" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <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/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','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>