| Previous changeset 45:28416ed17e41 (2017-04-24) Next changeset 47:6133bb91d065 (2017-04-24) |
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Commit message:
Uploaded |
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modified:
GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/tool_dependencies.xml |
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removed:
GRsetFromGEO/Untitled.R |
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| diff -r 28416ed17e41 -r 591f68d46899 GRsetFromGEO/GRsetFromGEO.xml --- a/GRsetFromGEO/GRsetFromGEO.xml Mon Apr 24 10:52:54 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.xml Mon Apr 24 11:15:37 2017 -0400 |
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| @@ -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:" /> |
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| diff -r 28416ed17e41 -r 591f68d46899 GRsetFromGEO/Untitled.R --- a/GRsetFromGEO/Untitled.R Mon Apr 24 10:52:54 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -require("minfi", quietly = TRUE) - -args <- commandArgs(trailingOnly = TRUE) -GSE = args[1] -output = args[2] - -GRset <- getGenomicRatioSetFromGEO(GSE) - -save(GRset,output) - |
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| diff -r 28416ed17e41 -r 591f68d46899 GRsetFromGEO/tool_dependencies.xml --- 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 |
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| b'@@ -1,10 +1,103 @@\n <?xml version="1.0"?>\n <tool_dependency>\n- <package name="minfi" version="1.16.0">\n- \t# TODO:\n- <repository changeset_revision="d0cee75b3e2e" name="package_minfi_1_16_0" owner="nturaga" toolshed="https://toolshed.g2.bx.psu.edu" />\n+ <package name="libcurl" version="7.35">\n+ <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n </package>\n <package name="R" version="3.2.1">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n+ </package>\n+ <package name="minfi" version="1.16.0">\n+ <install version="1.0">\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="libcurl" version="7.35" />\n+ </repository>\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1" />\n+ </repository>\n+ <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>\n+ <package>http://bioconductor.org/packages/release/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>\n+ <package>http://bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.4.8.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>\n+ <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/Biostrings_2.38.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/iterators_1.0.8.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.3.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/locfit_1.5-9.1.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/matrixStats_0.14.2.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/limma_3.26.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/registry_0.3.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/digest_0.6.9.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/stringi_1.0-1.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/magrittr_1.5.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/stringr_1.0.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/pkgmaker_0.22.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/rngtools_1.2.4.tar.gz</package>\n+ <package>https://depot.galaxyproject.or'..b' <package>https://depot.galaxyproject.org/package/noarch/nor1mix_1.2-1.tar.gz</package>\n+ <package>http://bioconductor.org/packages/release/bioc/src/contrib/multtest_2.26.0.tar.gz</package>\n+ <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/siggenes_1.44.0.tar.gz</package>\n+ <package>http://bioconductor.org/packages/release/bioc/src/contrib/preprocessCore_1.32.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/base64_1.1.tar.gz</package>\n+ <package>http://bioconductor.org/packages/release/bioc/src/contrib/illuminaio_0.12.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/mclust_5.0.2.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz</package>\n+ <package>http://bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.52.1.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/Rcpp_0.12.1.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/plyr_1.8.3.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/reshape_0.8.5.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/quadprog_1.5-5.tar.gz</package>\n+ <package>https://bioarchive.galaxyproject.org/GEOquery_2.35.7.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/colorspace_1.2-6.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/dichromat_2.0-0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/labeling_0.3.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/munsell_0.4.3.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/reshape2_1.4.1.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/gtable_0.2.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/scales_0.4.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/ggplot2_2.1.0.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/rgl_0.95.1441.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/ellipse_0.3-8.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/corpcor_1.6.8.tar.gz</package>\n+ <package>https://depot.galaxyproject.org/package/noarch/cluster_2.0.4.tar.gz</package>\n+ 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