Repository 'geo_data'
hg clone https://toolshed.g2.bx.psu.edu/repos/testtool/geo_data

Changeset 21:59122070e61d (2017-04-12)
Previous changeset 20:882e9c8498fa (2017-04-12) Next changeset 22:3381429d7391 (2017-04-12)
Commit message:
Uploaded
modified:
GRsetFromGEO/GRsetFromGEO.R
GRsetFromGEO/tool_dependencies.xml
b
diff -r 882e9c8498fa -r 59122070e61d GRsetFromGEO/GRsetFromGEO.R
--- a/GRsetFromGEO/GRsetFromGEO.R Wed Apr 12 13:00:22 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R Wed Apr 12 13:20:50 2017 -0400
[
@@ -1,3 +1,5 @@
+require("minfi", quietly = TRUE)
+
 options(warn = -1)
 options("download.file.method"="wget")
 
@@ -5,6 +7,6 @@
 GSE = args[1] 
 output = args[2] 
 
-GRset <- minfi::getGenomicRatioSetFromGEO(GSE)
+GRset <- getGenomicRatioSetFromGEO(GSE)
 
 save(GRset,file = output)
b
diff -r 882e9c8498fa -r 59122070e61d GRsetFromGEO/tool_dependencies.xml
--- a/GRsetFromGEO/tool_dependencies.xml Wed Apr 12 13:00:22 2017 -0400
+++ b/GRsetFromGEO/tool_dependencies.xml Wed Apr 12 13:20:50 2017 -0400
b
b'@@ -1,274 +1,9 @@\n <?xml version="1.0"?>\n <tool_dependency>\n-  <install version="1.0">\n-    <actions>\n-                <action type="setup_r_environment">\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://bioc.ism.ac.jp/packages/3.3/bioc/src/contrib/minfi_1.18.6.tar.gz</package>\n-                      <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n-                          https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n-                      </package>\n-                      <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n-                          https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n-                      </package>\n-                      <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n-                          https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n-                      </package>\n-                      <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n-                          https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz\n-                      </package>\n-                      <package sha256sum="7f1aa58085a030b7855a4e189bea2f17ff72333a1f884f0ab7f5af1fbe101397">\n-                          https://bioarchive.galaxyproject.org/GOSemSim_2.1.2.tar.gz\n-                      </package>\n-                      <package sha256sum="dc64ed09b8b5f8d66ed4936cde3491974d6bc5178dd259b6eab7ef3936aa5602">\n-                          https://depot.galaxyproject.org/software/igraph/igraph_1.0.1.tar.gz\n-                      </package>\n-                      <package sha256sum="f9e132c35d3af919cff291465d030817ff74e56eb6b2770390ae8566881b62ed">\n-                          https://bioarchive.galaxyproject.org/qvalue_2.7.0.tar.gz\n-                      </package>\n-                      <package sha256sum="6d3783610379be4c5676d9236cf66276a166b5b96c18f2759e9b219758959b6b">\n-                          https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.2.tar.gz\n-                      </package>\n-                      <package sha256sum="642b88fb1fce7bac72a0038ce532b65b8a79dffe826fec25033cf386ab630cd3">\n-                          https://depot.galaxyproject.org/software/scales/scales_0.4.1.tar.gz\n-                      </package>\n-                      <package sha256sum="51a74de64296d7cbed04a015a9f9725de95adb5e04301d1cd58190d7365fb104">\n-                          https://bioarchive.galaxyproject.org/biomaRt_2.31.3.tar.gz\n-                      </package>\n-                      <package sha256sum="801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f">\n-                          https://depot.galaxyproject.org/software/gtable/gtable_0.2.0.tar.gz\n-                      </package>\n-                      <package sha256sum="ed8a8bd0591223f742be80fd1cd8c4a9618d0f04011ec95c272b61ea45193104">\n-                          https://depot.galaxyproject.org/software/tibble/tibble_1.2.tar.gz\n-                      </package>\n-                      <package sha256sum="13738f55b2044184fe91f53d17516a445dfb508227527921218cda6f01f98dcb">\n-                          https://depot.galaxyproject.org/software/lazyeval/lazyeval_0.2.0.tar.gz\n-                      </package>\n-                      <package sha256sum="8097ec0e4868f6bf746f821cff7842f696e874bb3a84f1b2aa977ecd961c3e4e">\n-                          https://depot.galaxyproject.org/software/gdata/gdata_2.17.0.tar.gz\n-                      </package>\n-                      <package sha256sum="d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4">\n-                          https://depot.galaxyproject.org/software/caTools/caTo'..b'quadprog_1.5-5.tar.gz\n-                      </package>\n-                      <package sha256sum="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n-                          https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n-                      </package>\n-                      <package sha256sum="bee70645c7cc88250761092762a9d293b4644f311047baecf49fde766d3059bc">\n-                          https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz\n-                      </package>\n-                      <package sha256sum="c6133611cc991dfc17410d06a9ddcc6dcff0153bceffdf7d5a9b7dc42f31afa6">\n-                          https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz\n-                      </package>\n-                      <package sha256sum="cf61732ef9b38ecb6579055d1cd145198ad23a5a9ae4378f94a1494e6c56c884">\n-                          https://depot.galaxyproj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