|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="R" version="3.2.1">
|
|
|
4 <repository changeset_revision="3f2e129aae27" name="brenninc_r_oct9_2015" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
|
|
|
5 </package>
|
|
|
6 <!--package name="R_extended" version="0.0.1">
|
|
|
7 <install version="1.0">
|
|
|
8 <actions>
|
|
|
9 <action type="setup_r_environment">
|
|
|
10 <repository name="package_r_3_2_1" owner="brenninc" prior_installation_required="True" >
|
|
|
11 <package name="R" version="3.2.1" />
|
|
|
12 </repository>
|
|
|
13 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/BiocGenerics_0.14.0.tar.gz</package>
|
|
|
14 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/S4Vectors_0.6.6.tar.gz</package>
|
|
|
15 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/IRanges_2.2.9.tar.gz</package>
|
|
|
16 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/GenomeInfoDb_1.4.3.tar.gz</package>
|
|
|
17 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/XVector_0.8.0.tar.gz</package>
|
|
|
18 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/GenomicRanges_1.20.8.tar.gz</package>
|
|
|
19 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Rcpp_0.12.1.tar.gz</package>
|
|
|
20 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RcppArmadillo_0.6.100.0.0.tar.gz</package>
|
|
|
21 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Biobase_2.28.0.tar.gz</package>
|
|
|
22 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/lambda.r_1.1.7.tar.gz</package>
|
|
|
23 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/futile.options_1.0.0.tar.gz</package>
|
|
|
24 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/futile.logger_1.4.1.tar.gz</package>
|
|
|
25 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/snow_0.3-13.tar.gz</package>
|
|
|
26 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/BiocParallel_1.2.22.tar.gz</package>
|
|
|
27 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/DBI_0.3.1.tar.gz</package>
|
|
|
28 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RSQLite_1.0.0.tar.gz</package>
|
|
|
29 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/AnnotationDbi_1.30.1.tar.gz</package>
|
|
|
30 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/XML_3.98-1.3.tar.gz</package>
|
|
|
31 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/xtable_1.7-4.tar.gz</package>
|
|
|
32 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/annotate_1.46.1.tar.gz</package>
|
|
|
33 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/survival_2.38-3.tar.gz</package>
|
|
|
34 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/genefilter_1.50.0.tar.gz</package>
|
|
|
35 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/lattice_0.20-33.tar.gz</package>
|
|
|
36 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/locfit_1.5-9.1.tar.gz</package>
|
|
|
37 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RColorBrewer_1.1-2.tar.gz</package>
|
|
|
38 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/geneplotter_1.46.0.tar.gz</package>
|
|
|
39 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/plyr_1.8.3.tar.gz</package>
|
|
|
40 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/digest_0.6.8.tar.gz</package>
|
|
|
41 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/gtable_0.1.2.tar.gz</package>
|
|
|
42 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/stringi_0.5-5.tar.gz</package>
|
|
|
43 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/magrittr_1.5.tar.gz</package>
|
|
|
44 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/stringr_1.0.0.tar.gz</package>
|
|
|
45 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/reshape2_1.4.1.tar.gz</package>
|
|
|
46 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/dichromat_2.0-0.tar.gz</package>
|
|
|
47 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/colorspace_1.2-6.tar.gz</package>
|
|
|
48 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/munsell_0.4.2.tar.gz</package>
|
|
|
49 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/labeling_0.3.tar.gz</package>
|
|
|
50 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/scales_0.3.0.tar.gz</package>
|
|
|
51 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/proto_0.3-10.tar.gz</package>
|
|
|
52 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/MASS_7.3-44.tar.gz</package>
|
|
|
53 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/ggplot2_1.0.1.tar.gz</package>
|
|
|
54 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Formula_1.2-1.tar.gz</package>
|
|
|
55 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/latticeExtra_0.6-26.tar.gz</package>
|
|
|
56 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/cluster_2.0.3.tar.gz</package>
|
|
|
57 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/rpart_4.1-10.tar.gz</package>
|
|
|
58 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/nnet_7.3-11.tar.gz</package>
|
|
|
59 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/acepack_1.3-3.3.tar.gz</package>
|
|
|
60 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/foreign_0.8-66.tar.gz</package>
|
|
|
61 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/gridExtra_2.0.0.tar.gz</package>
|
|
|
62 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Hmisc_3.17-0.tar.gz</package>
|
|
|
63 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/DESeq2_1.8.2.tar.gz</package>
|
|
|
64 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/modeltools_0.2-21.tar.gz</package>
|
|
|
65 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/flexmix_2.3-13.tar.gz</package>
|
|
|
66 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/brew_1.0-6.tar.gz</package>
|
|
|
67 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Rook_1.1-1.tar.gz</package>
|
|
|
68 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/rjson_0.2.15.tar.gz</package>
|
|
|
69 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Cairo_1.5-9.tar.gz</package>
|
|
|
70 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/limma_3.24.15.tar.gz</package>
|
|
|
71 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/edgeR_3.10.5.tar.gz</package>
|
|
|
72 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RMTstat_0.3.tar.gz</package>
|
|
|
73 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Lmoments_1.1-6.tar.gz</package>
|
|
|
74 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/distillery_1.0-2.tar.gz</package>
|
|
|
75 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/nlme_3.1-122.tar.gz</package>
|
|
|
76 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Matrix_1.2-2.tar.gz</package>
|
|
|
77 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/mgcv_1.8-7.tar.gz</package>
|
|
|
78 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/minqa_1.2.4.tar.gz</package>
|
|
|
79 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/nloptr_1.0.4.tar.gz</package>
|
|
|
80 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RcppEigen_0.3.2.5.1.tar.gz</package>
|
|
|
81 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/lme4_1.1-10.tar.gz</package>
|
|
|
82 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/pbkrtest_0.4-2.tar.gz</package>
|
|
|
83 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/SparseM_1.7.tar.gz</package>
|
|
|
84 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/MatrixModels_0.4-1.tar.gz</package>
|
|
|
85 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/quantreg_5.19.tar.gz</package>
|
|
|
86 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/car_2.1-0.tar.gz</package>
|
|
|
87 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/extRemes_2.0-6.tar.gz</package>
|
|
|
88 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/pcaMethods_1.58.0.tar.gz</package>
|
|
|
89 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/scde_1.2.1.tar.gz</package>
|
|
|
90 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/evaluate_0.8.tar.gz</package>
|
|
|
91 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/formatR_1.2.1.tar.gz</package>
|
|
|
92 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/highr_0.5.1.tar.gz</package>
|
|
|
93 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/mime_0.4.tar.gz</package>
|
|
|
94 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/markdown_0.7.7.tar.gz</package>
|
|
|
95 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/yaml_2.1.13.tar.gz</package>
|
|
|
96 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/knitr_1.11.tar.gz</package>
|
|
|
97 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/proxy_0.4-15.tar.gz</package>
|
|
|
98 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/cba_0.2-15.tar.gz</package>
|
|
|
99 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/fastcluster_1.1.16.tar.gz</package>
|
|
|
100 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/dynamicTreeCut_1.62.tar.gz</package>
|
|
|
101 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/matrixStats_0.14.2.tar.gz</package>
|
|
|
102 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/impute_1.42.0.tar.gz</package>
|
|
|
103 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/codetools_0.2-14.tar.gz</package>
|
|
|
104 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/iterators_1.0.8.tar.gz</package>
|
|
|
105 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/foreach_1.4.3.tar.gz</package>
|
|
|
106 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/doParallel_1.0.10.tar.gz</package>
|
|
|
107 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/reshape_0.8.5.tar.gz</package>
|
|
|
108 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/preprocessCore_1.30.0.tar.gz</package>
|
|
|
109 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/GO.db_3.1.2.tar.gz</package>
|
|
|
110 <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/WGCNA_1.47.tar.gz</package>
|
|
|
111 </action>
|
|
|
112 </actions>
|
|
|
113 </install>
|
|
|
114 </package-->
|
|
|
115 </tool_dependency>
|