Mercurial > repos > stef > qdnaseq
changeset 8:b430d4b84233 draft
wget instead of download_by_url
| author | stef |
|---|---|
| date | Mon, 16 Jun 2014 07:43:06 -0400 |
| parents | 2671b48cc122 |
| children | 437bd8b88be2 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 38 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 16 07:43:06 2014 -0400 @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<tool_dependency> + + <set_environment version="1.0"> + <environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + + <package name="R" version="3.0.3"> + <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" /> + </package> + + <package name="bioc_qdnaseq" version="1.0.5"> + <install version="1.0"> + <actions> + <!--<action type="download_by_url"> + http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz + </action>--> + <action type="shell_command">wget http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/"> + <package name="R" version="3.0.3" /> + </repository> + </action> + <!-- <action type="shell_command">export R_LIBS=$INSTALL_DIR && R CMD INSTALL QDNAseq_1.0.5.tar.gz</action> --> + <action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action> + + <action type="set_environment"> + <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + + <readme> + Should install QDNAseq package from bioconductor. + </readme> + </package> + +</tool_dependency>