changeset 0:362a2224b1d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_deseq2_1_10_0 commit 77385ec02b79f527348aff01bd83a019e30f5f45

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Apr 25 10:01:56 2016 -0400
@@ -0,0 +1,211 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="d0bf97420fb5" 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="45b16a3ab504" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deseq2" version="1.10.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="d0bf97420fb5" 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="45b16a3ab504" name="package_libxml2_2_9_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libxml2" version="2.9.1" />
+                    </repository>
+                    <package sha256sum="d16ad5910aee6247990a19745511a5d50e19fa8c236000cbf99395e06c73c9f8">
+                        https://depot.galaxyproject.org/software/BiocGenerics/BiocGenerics_0.14.0_src_all.tar.gz
+                    </package>
+                    <package sha256sum="25f82ea9278cfc93b8dadb70fe3b6d114719ea4247c28178d699fde8cacd68f0">
+                        https://depot.galaxyproject.org/software/S4Vectors/S4Vectors_0.6.5_src_all.tar.gz
+                    </package>
+                    <package sha256sum="0609e1887e17ab75f8fcabb40e7c5995a4033c2c6e764e73bda8d35350561861">
+                        https://depot.galaxyproject.org/software/IRanges/IRanges_2.2.7_src_all.tar.gz
+                    </package>
+                    <package sha256sum="3d4ff22c6a11192ee1e313042ff0da4703b18c72f2247be73a0590769328d05a">
+                        https://depot.galaxyproject.org/software/GenomeInfoDb/GenomeInfoDb_1.4.2_src_all.tar.gz
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+                    <package sha256sum="64ca661349d7e25d8f2363901fa452b55d05780913025a5856a7b635166c1925">
+                        https://depot.galaxyproject.org/software/XVector/XVector_0.8.0_src_all.tar.gz
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+                    <package sha256sum="9d2bedd17a73864406d0284ddea2d28aef84c7c969b6924d8be2285d96f14e13">
+                        https://depot.galaxyproject.org/software/GenomicRanges/GenomicRanges_1.20.6_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/Rcpp/Rcpp_0.12.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/RcppArmadillo/RcppArmadillo_0.5.500.2.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/Biobase/Biobase_2.28.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/lambda.r/lambda.r_1.1.7_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/futile.options/futile.options_1.0.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/futile.logger/futile.logger_1.4.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/snow/snow_0.3-13_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/BiocParallel/BiocParallel_1.2.20_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/DBI/DBI_0.3.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/RSQLite/RSQLite_1.0.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/AnnotationDbi/AnnotationDbi_1.30.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/XML/XML_3.98-1.3_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/xtable/xtable_1.7-4_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/annotate/annotate_1.46.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/survival/survival_2.38-3_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/genefilter/genefilter_1.50.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/lattice/lattice_0.20-33_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/locfit/locfit_1.5-9.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/geneplotter/geneplotter_1.46.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/plyr/plyr_1.8.3_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/digest/digest_0.6.8_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/gtable/gtable_0.1.2_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/stringi/stringi_0.5-5_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/magrittr/magrittr_1.5_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/stringr/stringr_1.0.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/colorspace/colorspace_1.2-6_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/munsell/munsell_0.4.2_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/labeling/labeling_0.3_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/scales/scales_0.3.0_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/proto/proto_0.3-10_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/MASS/MASS_7.3-44_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/Formula/Formula_1.2-1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/latticeExtra/latticeExtra_0.6-26_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/cluster/cluster_2.0.3_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/rpart/rpart_4.1-10_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/nnet/nnet_7.3-11_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/foreign/foreign_0.8-66_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/Hmisc/Hmisc_3.16-0_src_all.tar.gz
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+                    <package sha256sum="9a823489b05f043ed6831d2045efbbaaec74aa61c0692f77893e59b7c7f3941f">
+                        https://bioarchive.galaxyproject.org/DESeq2_1.10.0.tar.gz
+                    </package>
+                    <!-- gplots dependency -->
+                    <package sha256sum="fa2b8351223369a13f4e922f13e8c836459a9522c775a455afd5e2b18941bb34">
+                        https://depot.galaxyproject.org/software/gtools/gtools_3.4.1_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/gdata/gdata_2.13.3_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/bitops/bitops_1.0-6_src_all.tar.gz
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+                        https://depot.galaxyproject.org/software/caTools/caTools_1.17.1_src_all.tar.gz
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+                    <package sha256sum="3f5fbda9201ea0dab4b5d30a8b857460a929502fc07e3fadc87445c746ce3fe5">
+                        https://depot.galaxyproject.org/software/KernSmooth/KernSmooth_2.23-13_src_all.tar.gz
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+                    <package sha256sum="8cb2ef4309f44eb049f0a8761d3b2aaf636e0ec2323942ec0c27fd8b4912abf9">
+                        https://depot.galaxyproject.org/software/gplots/gplots_2.14.2_src_all.tar.gz
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+
+                    <!-- wrapper dependency -->
+                    <package sha256sum="f920baa2a0ef7082155c8b666851af0c77534af8b2ca0cd067e7d56fdf3ec501">
+                        https://depot.galaxyproject.org/software/getopt/getopt_1.20.0_src_all.tar.gz
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+                    <package sha256sum="93d417f4eddb6fb7d679fbabb934b155de3965cf3d3e5ab03af69af5a0123357">
+                        https://depot.galaxyproject.org/software/rjson/rjson_0.2.14_src_all.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>