Mercurial > repos > stef > package_qdnaseq_1_0_5
comparison tool_dependencies.xml @ 18:14491b8d4d2b draft default tip
Uploaded
| author | stef |
|---|---|
| date | Thu, 06 Nov 2014 03:53:30 -0500 |
| parents | df8b1d258e35 |
| children |
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| 17:df8b1d258e35 | 18:14491b8d4d2b |
|---|---|
| 14 <install version="1.0"> | 14 <install version="1.0"> |
| 15 <actions> | 15 <actions> |
| 16 <action type="shell_command">echo "[DEBUG] Starting install actions"</action> | 16 <action type="shell_command">echo "[DEBUG] Starting install actions"</action> |
| 17 <action type="setup_r_environment"> | 17 <action type="setup_r_environment"> |
| 18 | 18 |
| 19 <!-- originally tried 3_1_0 but multiple errors --> | |
| 19 <!-- | 20 <!-- |
| 20 <repository name="package_r_3_1_0" owner="iuc"> | 21 <repository name="package_r_3_1_0" owner="iuc"> |
| 21 <package name="R" version="3.1.0" /> | 22 <package name="R" version="3.1.0" /> |
| 22 </repository> | 23 </repository> |
| 23 --> | 24 --> |
| 24 | 25 |
| 26 <!-- this one has to compile but works in all tests I did --> | |
| 25 <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 27 <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 26 <package name="R_3_1_1" version="3.1.1" /> | 28 <package name="R_3_1_1" version="3.1.1" /> |
| 27 </repository> | 29 </repository> |
| 28 | 30 |
| 29 <!-- | 31 <!-- |
| 30 <action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</action> | 32 <action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</action> |
| 31 --> | 33 --> |
| 32 | 34 |
| 33 <!-- | |
| 34 <package>http://path/to/R.methodsS3_1.6.1.tar.gz</package> | |
| 35 <package>http://path/to/matrixStats_0.10.0.tar.gz</package> | |
| 36 <package>http://path/to/R.oo_1.18.0.tar.gz</package> | |
| 37 <package>http://path/to/R.utils_1.32.4.tar.gz</package> | |
| 38 <package>http://path/to/BiocGenerics_0.10.0.tar.gz</package> | |
| 39 <package>http://path/to/Biobase_2.24.0.tar.gz</package> | |
| 40 <package>http://path/to/limma_3.20.5.tar.gz</package> | |
| 41 <package>http://path/to/marray_1.42.0.tar.gz</package> | |
| 42 <package>http://path/to/CGHbase_1.24.0.tar.gz</package> | |
| 43 <package>http://path/to/impute_1.38.1.tar.gz</package> | |
| 44 <package>http://path/to/DNAcopy_1.38.1.tar.gz</package> | |
| 45 <package>http://path/to/snow_0.3-13.tar.gz</package> | |
| 46 <package>http://path/to/snowfall_1.84-6.tar.gz</package> | |
| 47 <package>http://path/to/CGHcall_2.26.0.tar.gz</package> | |
| 48 <package>http://path/to/IRanges_1.22.9.tar.gz</package> | |
| 49 <package>http://path/to/GenomeInfoDb_1.0.2.tar.gz</package> | |
| 50 <package>http://path/to/XVector_0.4.0.tar.gz</package> | |
| 51 <package>http://path/to/GenomicRanges_1.16.3.tar.gz</package> | |
| 52 <package>http://path/to/zlibbioc_1.10.0.tar.gz</package> | |
| 53 <package>http://path/to/Biostrings_2.32.0.tar.gz</package> | |
| 54 <package>http://path/to/bitops_1.0-6.tar.gz</package> | |
| 55 <package>http://path/to/Rsamtools_1.16.1.tar.gz</package> | |
| 56 <package>http://path/to/QDNAseq_1.0.5.tar.gz</package> | |
| 57 --> | |
| 58 <!-- HERE all the packages hosted at bitbucket --> | 35 <!-- HERE all the packages hosted at bitbucket --> |
| 59 <!-- currently breaks at DNAcopy --> | 36 <!-- currently breaks at DNAcopy with R3.1.0 iuc dep pack --> |
| 60 | |
| 61 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.methodsS3_1.6.1.tar.gz</package> | 37 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.methodsS3_1.6.1.tar.gz</package> |
| 62 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/matrixStats_0.10.0.tar.gz</package> | 38 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/matrixStats_0.10.0.tar.gz</package> |
| 63 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.oo_1.18.0.tar.gz</package> | 39 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.oo_1.18.0.tar.gz</package> |
| 64 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.utils_1.32.4.tar.gz</package> | 40 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.utils_1.32.4.tar.gz</package> |
| 65 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/BiocGenerics_0.10.0.tar.gz</package> | 41 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/BiocGenerics_0.10.0.tar.gz</package> |
| 66 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biobase_2.24.0.tar.gz</package> | 42 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biobase_2.24.0.tar.gz</package> |
| 67 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/limma_3.20.5.tar.gz</package> | 43 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/limma_3.20.5.tar.gz</package> |
| 68 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/marray_1.42.0.tar.gz</package> | 44 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/marray_1.42.0.tar.gz</package> |
| 69 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHbase_1.24.0.tar.gz</package> | 45 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHbase_1.24.0.tar.gz</package> |
| 70 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/impute_1.38.1.tar.gz</package> | 46 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/impute_1.38.1.tar.gz</package> |
| 71 | |
| 72 | |
| 73 | |
| 74 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/DNAcopy_1.38.1.tar.gz</package> | 47 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/DNAcopy_1.38.1.tar.gz</package> |
| 75 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snow_0.3-13.tar.gz</package> | 48 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snow_0.3-13.tar.gz</package> |
| 76 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snowfall_1.84-6.tar.gz</package> | 49 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snowfall_1.84-6.tar.gz</package> |
| 77 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHcall_2.26.0.tar.gz</package> | 50 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHcall_2.26.0.tar.gz</package> |
| 78 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/IRanges_1.22.9.tar.gz</package> | 51 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/IRanges_1.22.9.tar.gz</package> |
| 82 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/zlibbioc_1.10.0.tar.gz</package> | 55 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/zlibbioc_1.10.0.tar.gz</package> |
| 83 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biostrings_2.32.1.tar.gz</package> | 56 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biostrings_2.32.1.tar.gz</package> |
| 84 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/bitops_1.0-6.tar.gz</package> | 57 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/bitops_1.0-6.tar.gz</package> |
| 85 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Rsamtools_1.16.1.tar.gz</package> | 58 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Rsamtools_1.16.1.tar.gz</package> |
| 86 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/QDNAseq_1.0.5.tar.gz</package> | 59 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/QDNAseq_1.0.5.tar.gz</package> |
| 87 | |
| 88 | 60 |
| 89 </action> | 61 </action> |
| 90 <action type="shell_command">echo "[DEBUG] ...done with install actions"</action> | 62 <action type="shell_command">echo "[DEBUG] ...done with install actions"</action> |
| 91 </actions> | 63 </actions> |
| 92 </install> | 64 </install> |