changeset 0:00b14423d00f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_deseq2_1_8_2 commit c196ca939107154dbcfa84ed34fb01655f4fc59f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 14 03:17:57 2015 -0400
@@ -0,0 +1,93 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="e46a7803f17b" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libxml2" version="2.9.1">
+        <repository changeset_revision="e5475acebd6e" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deseq2" version="1.8.2">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="e46a7803f17b" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.2.1" />
+                    </repository>
+                    <!-- libxml2 needs to be sourced after R because R also was compiled against a different version of libxml2 -->
+                    <repository changeset_revision="e5475acebd6e" name="package_libxml2_2_9_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libxml2" version="2.9.1" />
+                    </repository>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/BiocGenerics_0.14.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/S4Vectors_0.6.5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/IRanges_2.2.7.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/GenomeInfoDb_1.4.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/XVector_0.8.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/GenomicRanges_1.20.6.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/Rcpp_0.12.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/RcppArmadillo_0.5.500.2.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/Biobase_2.28.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/lambda.r_1.1.7.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/futile.options_1.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/futile.logger_1.4.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/snow_0.3-13.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/BiocParallel_1.2.20.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/DBI_0.3.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/RSQLite_1.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/AnnotationDbi_1.30.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/XML_3.98-1.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/xtable_1.7-4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/annotate_1.46.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/survival_2.38-3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/genefilter_1.50.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/lattice_0.20-33.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/geneplotter_1.46.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/plyr_1.8.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/digest_0.6.8.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/gtable_0.1.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/stringi_0.5-5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/magrittr_1.5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/stringr_1.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/reshape2_1.4.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/dichromat_2.0-0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/colorspace_1.2-6.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/munsell_0.4.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/labeling_0.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/scales_0.3.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/proto_0.3-10.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/MASS_7.3-44.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/ggplot2_1.0.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/Formula_1.2-1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/latticeExtra_0.6-26.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/cluster_2.0.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/rpart_4.1-10.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/nnet_7.3-11.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/acepack_1.3-3.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/foreign_0.8-66.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/gridExtra_2.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/Hmisc_3.16-0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2_1_8_2/DESeq2_1.8.2.tar.gz</package>
+                    <!-- gplots dependency -->
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/gtools_3.4.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/gdata_2.13.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/bitops_1.0-6.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/caTools_1.17.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/KernSmooth_2.23-13.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/gplots_2.14.2.tar.gz</package>
+
+                    <!-- wrapper dependency -->
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/getopt_1.20.0.tar.gz</package>
+                    <package sha256sum="93d417f4eddb6fb7d679fbabb934b155de3965cf3d3e5ab03af69af5a0123357">https://github.com/bgruening/download_store/raw/master/DESeq2_1_8_2/rjson_0.2.14.tar.gz</package>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="DESEQ2_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        Differential gene expression analysis based on the negative binomial distribution.
+        http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
+        </readme>
+    </package>
+</tool_dependency>