Mercurial > repos > stef > package_qdnaseq_1_0_5
changeset 2:42096296e06f draft
Uploaded
| author | stef |
|---|---|
| date | Mon, 06 Oct 2014 10:30:19 -0400 |
| parents | 3fcdbbc43d62 |
| children | 8473e3b3c386 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 24 insertions(+), 46 deletions(-) [+] |
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--- a/tool_dependencies.xml Thu Jun 19 06:02:41 2014 -0400 +++ b/tool_dependencies.xml Mon Oct 06 10:30:19 2014 -0400 @@ -1,49 +1,27 @@ <?xml version="1.0"?> <tool_dependency> - <!-- - <package name="R" version="3.1.0"> - <repository name="package_r_3_1_0" owner="" prior_installation_required="True" /> - </package> - <package name="qdnaseq" version="1.0.5"> - <install version="1.0"> - <actions> - <action type="shell_command">echo "[DEBUG] ..."</action> - <action type="setup_r_environment"> - - <repository name="package_r_3_1_0" owner=""> - <package name="R" version="3.1.0" /> - </repository> - - <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> - - </action> - </actions> - </install> - <readme> - Prepares R Bioconductor package "QDNAseq" and all of its dependencies. - </readme> - </package> - --> + + <package name="samtools" version="0.1.18"> + <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" --> + <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" --> + + <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" /> + </package> + + <!-- + <package name="qdnaseq" version="1.0.5"> + <repository name="package_qdnaseq_1_0_5" owner="stef"/> + </package> + --> + + <!-- + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + --> + </tool_dependency>