|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
3
|
3
|
|
|
4 <package name="R" version="3.1.0">
|
|
|
5 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
|
|
|
6 </package>
|
|
|
7 <package name="qdnaseq" version="1.0.5">
|
|
|
8 <install version="1.0">
|
|
|
9 <actions>
|
|
|
10 <action type="shell_command">echo "[DEBUG] ...before"</action>
|
|
|
11 <action type="setup_r_environment">
|
|
|
12
|
|
|
13 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
|
|
|
14 <package name="R" version="3.1.0" />
|
|
|
15 </repository>
|
|
6
|
16 <!--
|
|
5
|
17 <package>http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</package>
|
|
4
|
18 <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.9.tar.gz</package>
|
|
|
19 <package>http://bioconductor.org/packages/release/bioc/src/contrib/Rsamtools_1.16.1.tar.gz</package>
|
|
6
|
20 -->
|
|
2
|
21
|
|
6
|
22 <package>http://cran.fhcrc.org/src/contrib/R.methodsS3_1.6.1.tar.gz</package>
|
|
|
23 <package>http://cran.fhcrc.org/src/contrib/matrixStats_0.10.0.tar.gz</package>
|
|
|
24 <package>http://cran.fhcrc.org/src/contrib/R.oo_1.18.0.tar.gz</package>
|
|
7
|
25 <package>http://cran.fhcrc.org/src/contrib/R.utils_1.33.0.tar.gz</package>
|
|
6
|
26 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocGenerics_0.10.0.tar.gz</package>
|
|
|
27 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Biobase_2.24.0.tar.gz</package>
|
|
8
|
28 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/limma_3.20.9.tar.gz</package>
|
|
6
|
29 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/marray_1.42.0.tar.gz</package>
|
|
|
30 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/CGHbase_1.24.0.tar.gz</package>
|
|
|
31 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/impute_1.38.1.tar.gz</package>
|
|
|
32 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/DNAcopy_1.38.1.tar.gz</package>
|
|
|
33 <package>http://cran.fhcrc.org/src/contrib/snow_0.3-13.tar.gz</package>
|
|
|
34 <package>http://cran.fhcrc.org/src/contrib/snowfall_1.84-6.tar.gz</package>
|
|
|
35 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/CGHcall_2.26.0.tar.gz</package>
|
|
8
|
36 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/IRanges_1.22.10.tar.gz</package>
|
|
6
|
37 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomeInfoDb_1.0.2.tar.gz</package>
|
|
|
38 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/XVector_0.4.0.tar.gz</package>
|
|
|
39 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicRanges_1.16.4.tar.gz</package>
|
|
|
40 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/zlibbioc_1.10.0.tar.gz</package>
|
|
|
41 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Biostrings_2.32.1.tar.gz</package>
|
|
|
42 <package>http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz</package>
|
|
|
43 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Rsamtools_1.16.1.tar.gz</package>
|
|
|
44 <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</package>
|
|
8
|
45
|
|
3
|
46 <!--
|
|
|
47 <package>http://path/to/R.methodsS3_1.6.1.tar.gz</package>
|
|
|
48 <package>http://path/to/matrixStats_0.10.0.tar.gz</package>
|
|
|
49 <package>http://path/to/R.oo_1.18.0.tar.gz</package>
|
|
|
50 <package>http://path/to/R.utils_1.32.4.tar.gz</package>
|
|
|
51 <package>http://path/to/BiocGenerics_0.10.0.tar.gz</package>
|
|
|
52 <package>http://path/to/Biobase_2.24.0.tar.gz</package>
|
|
|
53 <package>http://path/to/limma_3.20.5.tar.gz</package>
|
|
|
54 <package>http://path/to/marray_1.42.0.tar.gz</package>
|
|
|
55 <package>http://path/to/CGHbase_1.24.0.tar.gz</package>
|
|
|
56 <package>http://path/to/impute_1.38.1.tar.gz</package>
|
|
|
57 <package>http://path/to/DNAcopy_1.38.1.tar.gz</package>
|
|
|
58 <package>http://path/to/snow_0.3-13.tar.gz</package>
|
|
|
59 <package>http://path/to/snowfall_1.84-6.tar.gz</package>
|
|
|
60 <package>http://path/to/CGHcall_2.26.0.tar.gz</package>
|
|
|
61 <package>http://path/to/IRanges_1.22.9.tar.gz</package>
|
|
|
62 <package>http://path/to/GenomeInfoDb_1.0.2.tar.gz</package>
|
|
|
63 <package>http://path/to/XVector_0.4.0.tar.gz</package>
|
|
|
64 <package>http://path/to/GenomicRanges_1.16.3.tar.gz</package>
|
|
|
65 <package>http://path/to/zlibbioc_1.10.0.tar.gz</package>
|
|
|
66 <package>http://path/to/Biostrings_2.32.0.tar.gz</package>
|
|
|
67 <package>http://path/to/bitops_1.0-6.tar.gz</package>
|
|
|
68 <package>http://path/to/Rsamtools_1.16.1.tar.gz</package>
|
|
|
69 <package>http://path/to/QDNAseq_1.0.5.tar.gz</package>
|
|
|
70 -->
|
|
|
71
|
|
|
72 </action>
|
|
|
73 <action type="shell_command">echo "[DEBUG] ...after"</action>
|
|
|
74 </actions>
|
|
|
75 </install>
|
|
|
76 <readme>
|
|
|
77 Prepares R Bioconductor package "QDNAseq" and all of its dependencies.
|
|
|
78 </readme>
|
|
|
79 </package>
|
|
0
|
80 </tool_dependency>
|
