Mercurial > repos > stef > package_qdnaseq_1_0_5
changeset 3:8473e3b3c386 draft
Uploaded
| author | stef |
|---|---|
| date | Mon, 06 Oct 2014 10:47:16 -0400 |
| parents | 42096296e06f |
| children | 1aec50e7e4b7 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 49 insertions(+), 23 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Mon Oct 06 10:30:19 2014 -0400 +++ b/tool_dependencies.xml Mon Oct 06 10:47:16 2014 -0400 @@ -1,27 +1,53 @@ <?xml version="1.0"?> <tool_dependency> - - <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> + + <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"> + <install version="1.0"> + <actions> + <action type="shell_command">echo "[DEBUG] ...before"</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"> + <package name="R" version="3.1.0" /> + </repository> + + <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.9REMOVE.tar.gz</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> - --> - + <!-- + <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> + <action type="shell_command">echo "[DEBUG] ...after"</action> + </actions> + </install> + <readme> + Prepares R Bioconductor package "QDNAseq" and all of its dependencies. + </readme> + </package> </tool_dependency>