Mercurial > repos > stef > qdnaseq
changeset 23:5f8b99ae75ef draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 18 Jun 2014 04:46:56 -0400 |
| parents | 5e5611bc7497 |
| children | 9f4e0192de10 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 11 insertions(+), 57 deletions(-) [+] |
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--- a/tool_dependencies.xml Tue Jun 17 05:35:22 2014 -0400 +++ b/tool_dependencies.xml Wed Jun 18 04:46:56 2014 -0400 @@ -1,59 +1,13 @@ <?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="shell_command">echo "[DEBUG] INSTALL DIR: $INSTALL_DIR"</action> - <action type="shell_command">echo "[DEBUG] REPOS INSTALL DIR: $REPOSITORY_INSTALL_DIR"</action> - - <action type="shell_command">echo "[DEBUG] BEFORE:" && pwd</action> - <action type="shell_command">echo "[DEBUG] DIR LISTING:" && ls -l</action> - <action type="shell_command">echo "[DEBUG] DIR LISTING ONE UP:" && ls -l ../</action> - <!-- - <action type="move_file"> - <source>../QDNAseq.R</source> - <destination>./</destination> - </action> - --> - - <action type="shell_command">echo "[DEBUG] AFTER:" && pwd</action> - <action type="shell_command">echo "[DEBUG] DIR LISTING:" && ls -l</action> - - <action type="set_environment_for_install"> - <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/"> - <package name="R" version="3.0.3" /> - </repository> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action> - - <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action> - - <action type="shell_command">echo "[DEBUG] WORKING DIR:" && pwd</action> - <action type="shell_command">echo "[DEBUG] DIR LISTING:" && ls -l</action> - - <action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action> - <!-- -<action type="shell_command">export R_LIBS=$INSTALL_DIR && R CMD INSTALL --> <!--build QDNAseq_1.0.5.tar.gz</action> - --> - <!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>--> - </actions> - </install> - - <readme> - Should install QDNAseq package from bioconductor. - </readme> - </package> - -</tool_dependency> + <!-- There is no R 3.1.0 package yet which is required due to bioconductor 2.14 package --> + <!-- As soon as it is available the dependencies will be set via "package_qdnaseq_1_0_5" --> + <!-- + <package name="R_3_1_0" version="3.1.0"> + <repository name="package_r_3_1_0" owner="iuc"/> + </package> + <package name="qdnaseq" version="1.0.5"> + <repository name="package_qdnaseq_1_0_5" owner="stef"/> + </package> + --> +</tool_dependency>