Mercurial > repos > pavanvidem > dexseq

changeset 9:56177132cee2 draft

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Uploaded
author pavanvidem
date Mon, 31 Aug 2015 05:25:40 -0400
parents b3101052013f
children d9d8a26d80bf
files tool_dependencies.xml
diffstat 1 files changed, 66 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 28 11:34:17 2015 -0400
+++ b/tool_dependencies.xml	Mon Aug 31 05:25:40 2015 -0400
@@ -1,38 +1,80 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R" version="3.1.0">
-        <repository changeset_revision="613002a3ad4c" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="R" version="3.2.0">
+        <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="libxml2" version="2.9.1">
-        <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="deseq2" version="1.6.1">
-        <repository changeset_revision="5beee6b62be7" name="package_deseq2_1_6_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="dexseq" version="1.14.1">
+    <package name="DEXSeq" version="1.14.2">
         <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
-                    <repository changeset_revision="613002a3ad4c" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="R" version="3.1.0" />
-                    </repository>
-                    <repository changeset_revision="5beee6b62be7" name="package_deseq2_1_6_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="deseq2" version="1.6.1" />
+                    <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.2.0" />
                     </repository>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/bitops_1.0-6.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/RCurl_1.95-4.7.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/zlibbioc_1.14.0.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/hwriter_1.3.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/statmod_1.4.21.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/S4Vectors_0.6.3.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/Biostrings_2.36.4.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/biomaRt_2.24.0.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.1/Rsamtools_1.20.4.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/lambda.r_1.1.7.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/futile.options_1.0.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/futile.logger_1.4.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/snow_0.3-13.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/BiocParallel_1.2.20.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/BiocGenerics_0.14.0.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/Biobase_2.28.0.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/S4Vectors_0.6.3.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/IRanges_2.2.7.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/GenomeInfoDb_1.4.2.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/XVector_0.8.0.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/GenomicRanges_1.20.5.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/Rcpp_0.12.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/RcppArmadillo_0.5.400.2.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/DBI_0.3.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/RSQLite_1.0.0.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/AnnotationDbi_1.30.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/XML_3.98-1.3.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/xtable_1.7-4.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/annotate_1.46.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/survival_2.38-3.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/genefilter_1.50.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/lattice_0.20-33.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/geneplotter_1.46.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/plyr_1.8.3.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/digest_0.6.8.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/gtable_0.1.2.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/stringi_0.5-5.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/stringr_1.0.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/reshape2_1.4.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/dichromat_2.0-0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/colorspace_1.2-6.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/munsell_0.4.2.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/labeling_0.3.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/scales_0.3.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/proto_0.3-10.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/MASS_7.3-43.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/ggplot2_1.0.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/Formula_1.2-1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/latticeExtra_0.6-26.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/cluster_2.0.3.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/rpart_4.1-10.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/nnet_7.3-10.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/foreign_0.8-66.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/gridExtra_2.0.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/Hmisc_3.16-0.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/DESeq2_1.8.1.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/bitops_1.0-6.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/RCurl_1.95-4.7.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/biomaRt_2.24.0.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/hwriter_1.3.2.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/zlibbioc_1.14.0.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/Biostrings_2.36.4.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/Rsamtools_1.20.4.tar.gz</package>
+                    <package>http://cran.rstudio.com/src/contrib/statmod_1.4.21.tar.gz</package>
+                    <package>http://bioarchive.galaxyproject.org/DEXSeq_1.14.2.tar.gz</package>
                 </action>
             </actions>
         </install>
         <readme>
-        Differential exon usage based on the negative binomial distribution.
+            DEXSeq in version
         </readme>
     </package>
 </tool_dependency>