Mercurial > repos > stef > package_qdnaseq_1_0_5
changeset 18:14491b8d4d2b draft default tip
Uploaded
| author | stef |
|---|---|
| date | Thu, 06 Nov 2014 03:53:30 -0500 |
| parents | df8b1d258e35 |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 3 insertions(+), 31 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Nov 05 11:21:00 2014 -0500 +++ b/tool_dependencies.xml Thu Nov 06 03:53:30 2014 -0500 @@ -16,12 +16,14 @@ <action type="shell_command">echo "[DEBUG] Starting install actions"</action> <action type="setup_r_environment"> + <!-- originally tried 3_1_0 but multiple errors --> <!-- <repository name="package_r_3_1_0" owner="iuc"> <package name="R" version="3.1.0" /> </repository> --> + <!-- this one has to compile but works in all tests I did --> <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="R_3_1_1" version="3.1.1" /> </repository> @@ -30,34 +32,8 @@ <action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</action> --> - <!-- - <package>http://path/to/R.methodsS3_1.6.1.tar.gz</package> - <package>http://path/to/matrixStats_0.10.0.tar.gz</package> - <package>http://path/to/R.oo_1.18.0.tar.gz</package> - <package>http://path/to/R.utils_1.32.4.tar.gz</package> - <package>http://path/to/BiocGenerics_0.10.0.tar.gz</package> - <package>http://path/to/Biobase_2.24.0.tar.gz</package> - <package>http://path/to/limma_3.20.5.tar.gz</package> - <package>http://path/to/marray_1.42.0.tar.gz</package> - <package>http://path/to/CGHbase_1.24.0.tar.gz</package> - <package>http://path/to/impute_1.38.1.tar.gz</package> - <package>http://path/to/DNAcopy_1.38.1.tar.gz</package> - <package>http://path/to/snow_0.3-13.tar.gz</package> - <package>http://path/to/snowfall_1.84-6.tar.gz</package> - <package>http://path/to/CGHcall_2.26.0.tar.gz</package> - <package>http://path/to/IRanges_1.22.9.tar.gz</package> - <package>http://path/to/GenomeInfoDb_1.0.2.tar.gz</package> - <package>http://path/to/XVector_0.4.0.tar.gz</package> - <package>http://path/to/GenomicRanges_1.16.3.tar.gz</package> - <package>http://path/to/zlibbioc_1.10.0.tar.gz</package> - <package>http://path/to/Biostrings_2.32.0.tar.gz</package> - <package>http://path/to/bitops_1.0-6.tar.gz</package> - <package>http://path/to/Rsamtools_1.16.1.tar.gz</package> - <package>http://path/to/QDNAseq_1.0.5.tar.gz</package> - --> <!-- HERE all the packages hosted at bitbucket --> - <!-- currently breaks at DNAcopy --> - + <!-- currently breaks at DNAcopy with R3.1.0 iuc dep pack --> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.methodsS3_1.6.1.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/matrixStats_0.10.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.oo_1.18.0.tar.gz</package> @@ -68,9 +44,6 @@ <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/marray_1.42.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHbase_1.24.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/impute_1.38.1.tar.gz</package> - - - <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/DNAcopy_1.38.1.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snow_0.3-13.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snowfall_1.84-6.tar.gz</package> @@ -84,7 +57,6 @@ <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/bitops_1.0-6.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Rsamtools_1.16.1.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/QDNAseq_1.0.5.tar.gz</package> - </action> <action type="shell_command">echo "[DEBUG] ...done with install actions"</action>