Mercurial > repos > dpryan79 > package_deseq2_1_2_10_test

changeset 2:d3d4bda07663 draft

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Uploaded
author dpryan79
date Tue, 08 Mar 2016 07:16:56 -0500
parents ab822f7635bb
children f6e99ba0f769
files tool_dependencies.xml
diffstat 1 files changed, 43 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Mar 08 07:16:56 2016 -0500
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.0.3">
+        <repository changeset_revision="9a289bea9051" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deseq2" version="1.2.10">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+
+                    <repository changeset_revision="9a289bea9051" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.0.3" />
+                    </repository>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/getopt_1.20.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/BiocGenerics_0.8.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/IRanges_1.20.6.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/XVector_0.2.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/XVector_0.2.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/GenomicRanges_1.14.4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/Rcpp_0.11.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/RcppArmadillo_0.4.000.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/Biobase_2.22.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/DBI_0.2-7.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/RSQLite_0.11.4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/AnnotationDbi_1.24.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/xtable_1.7-1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/XML_3.98-1.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/annotate_1.40.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/genefilter_1.44.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/RColorBrewer_1.0-5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/DESeq2_1.2.10.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/rjson_0.2.13.tar.gz</package>
+                </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>