Mercurial > repos > testtool > geo_data

changeset 46:591f68d46899 draft

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Uploaded
author testtool
date Mon, 24 Apr 2017 11:15:37 -0400
parents 28416ed17e41
children 6133bb91d065
files GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/Untitled.R GRsetFromGEO/tool_dependencies.xml
diffstat 3 files changed, 97 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Apr 24 10:52:54 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Mon Apr 24 11:15:37 2017 -0400
@@ -4,7 +4,6 @@
   </description>
   <requirements>
     <requirement type="package" version="3.2.1">R</requirement>
-    <requirement type="package" version="1.16.0">minfi</requirement>
      </requirements>
 <stdio>
    <exit_code range="1:" />
--- a/GRsetFromGEO/Untitled.R	Mon Apr 24 10:52:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-require("minfi", quietly = TRUE)
-
-args <- commandArgs(trailingOnly = TRUE)
-GSE = args[1] 
-output = args[2] 
-
-GRset <- getGenomicRatioSetFromGEO(GSE)
-
-save(GRset,output)
-
--- a/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 10:52:54 2017 -0400
+++ b/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 11:15:37 2017 -0400
@@ -1,10 +1,103 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="minfi" version="1.16.0">
-    	# TODO:
-        <repository changeset_revision="d0cee75b3e2e" name="package_minfi_1_16_0" owner="nturaga" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="libcurl" version="7.35">
+        <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.2.1">
-        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <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="minfi" version="1.16.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libcurl" version="7.35" />
+                    </repository>
+                    <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>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.4.8.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Biostrings_2.38.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/iterators_1.0.8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/matrixStats_0.14.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/limma_3.26.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/registry_0.3.tar.gz</package>
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+                    <package>https://depot.galaxyproject.org/package/noarch/magrittr_1.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/stringr_1.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/pkgmaker_0.22.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/rngtools_1.2.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/doRNG_1.6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/DBI_0.3.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RSQLite_1.0.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz</package>
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+                    <package>https://depot.galaxyproject.org/package/noarch/lambda.r_1.1.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/futile.options_1.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/futile.logger_1.4.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/snow_0.3-13.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/BiocParallel_1.3.54.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Rsamtools_1.22.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/SummarizedExperiment_1.0.2.tar.gz</package>
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+                    <package>https://bioarchive.galaxyproject.org/bumphunter_1.10.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/beanplot_1.2.tar.gz</package>
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+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/multtest_2.26.0.tar.gz</package>
+                    <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/siggenes_1.44.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/preprocessCore_1.32.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/base64_1.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/illuminaio_0.12.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/mclust_5.0.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz</package>
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+                    <package>https://depot.galaxyproject.org/package/noarch/plyr_1.8.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/reshape_0.8.5.tar.gz</package>
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+                    <package>https://depot.galaxyproject.org/package/noarch/igraph_1.0.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/mixOmics_5.2.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/minfi_1.16.0.tar.gz</package>
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+                    <package>https://bioconductor.org/packages/release/data/experiment/src/contrib/FlowSorted.Blood.450k_1.8.0.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
     </package>
 </tool_dependency>