Mercurial > repos > stef > package_qdnaseq_1_0_5
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author | stef |
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date | Thu, 06 Nov 2014 03:53:30 -0500 |
parents | df8b1d258e35 |
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<?xml version="1.0"?> <tool_dependency> <!-- <package name="R" version="3.1.0"> <repository name="package_r_3_1_0" owner="iuc" prior_installation_required="True" /> </package> --> <package name="R_3_1_1 " version="3.1.1"> <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="qdnaseq" version="1.0.5"> <install version="1.0"> <actions> <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> <!-- <action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</action> --> <!-- HERE all the packages hosted at bitbucket --> <!-- 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> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.utils_1.32.4.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/BiocGenerics_0.10.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biobase_2.24.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/limma_3.20.5.tar.gz</package> <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> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHcall_2.26.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/IRanges_1.22.9.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/GenomeInfoDb_1.0.2.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/XVector_0.4.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/GenomicRanges_1.16.4.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/zlibbioc_1.10.0.tar.gz</package> <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biostrings_2.32.1.tar.gz</package> <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> </actions> </install> <readme> Prepares R Bioconductor package "QDNAseq" and all of its dependencies. </readme> </package> </tool_dependency>