Mercurial > repos > stef > package_qdnaseq_1_0_5
changeset 12:f44792741a2f draft
Uploaded
author | stef |
---|---|
date | Wed, 05 Nov 2014 09:48:00 -0500 |
parents | 4a3ff383a680 |
children | 657b651aa0c3 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 20 insertions(+), 36 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Oct 27 06:39:51 2014 -0400 +++ b/tool_dependencies.xml Wed Nov 05 09:48:00 2014 -0500 @@ -1,55 +1,36 @@ <?xml version="1.0"?> <tool_dependency> + <!-- <package name="R" version="3.1.0"> - <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository name="package_r_3_1_0" owner="iuc" prior_installation_required="True" /> </package> + --> + <package name="R" 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] ...before"</action> + <action type="shell_command">echo "[DEBUG] Starting install actions"</action> <action type="setup_r_environment"> - <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <!-- + <repository name="package_r_3_1_0" owner="iuc"> <package name="R" version="3.1.0" /> </repository> - <!-- - <package>http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</package> - <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.9.tar.gz</package> - <package>http://bioconductor.org/packages/release/bioc/src/contrib/Rsamtools_1.16.1.tar.gz</package> - --> - <!-- - <package>http://cran.fhcrc.org/src/contrib/R.methodsS3_1.6.1.tar.gz</package> - <package>http://cran.fhcrc.org/src/contrib/matrixStats_0.10.0.tar.gz</package> - <package>http://cran.fhcrc.org/src/contrib/R.oo_1.18.0.tar.gz</package> - <package>http://cran.fhcrc.org/src/contrib/R.utils_1.33.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocGenerics_0.10.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Biobase_2.24.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/limma_3.20.9.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/marray_1.42.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/CGHbase_1.24.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/impute_1.38.1.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/DNAcopy_1.38.1.tar.gz</package> --> + <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="R" version="3.1.1" /> + </repository> + <!-- - <package>http://cran.fhcrc.org/src/contrib/snow_0.3-13.tar.gz</package> - <package>http://cran.fhcrc.org/src/contrib/snowfall_1.84-6.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/CGHcall_2.26.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/IRanges_1.22.10.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomeInfoDb_1.0.2.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/XVector_0.4.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicRanges_1.16.4.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/zlibbioc_1.10.0.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Biostrings_2.32.1.tar.gz</package> - <package>http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Rsamtools_1.16.1.tar.gz</package> - <package>http://bioconductor.org/packages/2.14/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</package> + <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> @@ -74,6 +55,9 @@ <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 --> + <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> @@ -102,7 +86,7 @@ --> </action> - <action type="shell_command">echo "[DEBUG] ...after"</action> + <action type="shell_command">echo "[DEBUG] ...done with install actions"</action> </actions> </install> <readme>