Mercurial > repos > stef > qdnaseq
comparison tool_dependencies.xml @ 23:5f8b99ae75ef draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 18 Jun 2014 04:46:56 -0400 |
| parents | 5e5611bc7497 |
| children | 45051afbeff4 |
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| 22:5e5611bc7497 | 23:5f8b99ae75ef |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 | 3 <!-- There is no R 3.1.0 package yet which is required due to bioconductor 2.14 package --> |
| 4 <set_environment version="1.0"> | 4 <!-- As soon as it is available the dependencies will be set via "package_qdnaseq_1_0_5" --> |
| 5 <environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> | 5 <!-- |
| 6 </set_environment> | 6 <package name="R_3_1_0" version="3.1.0"> |
| 7 | 7 <repository name="package_r_3_1_0" owner="iuc"/> |
| 8 <package name="R" version="3.0.3"> | 8 </package> |
| 9 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" /> | 9 <package name="qdnaseq" version="1.0.5"> |
| 10 </package> | 10 <repository name="package_qdnaseq_1_0_5" owner="stef"/> |
| 11 | 11 </package> |
| 12 <package name="bioc_qdnaseq" version="1.0.5"> | 12 --> |
| 13 <install version="1.0"> | 13 </tool_dependency> |
| 14 <actions> | |
| 15 <action type="shell_command">echo "[DEBUG] INSTALL DIR: $INSTALL_DIR"</action> | |
| 16 <action type="shell_command">echo "[DEBUG] REPOS INSTALL DIR: $REPOSITORY_INSTALL_DIR"</action> | |
| 17 | |
| 18 <action type="shell_command">echo "[DEBUG] BEFORE:" && pwd</action> | |
| 19 <action type="shell_command">echo "[DEBUG] DIR LISTING:" && ls -l</action> | |
| 20 <action type="shell_command">echo "[DEBUG] DIR LISTING ONE UP:" && ls -l ../</action> | |
| 21 <!-- | |
| 22 <action type="move_file"> | |
| 23 <source>../QDNAseq.R</source> | |
| 24 <destination>./</destination> | |
| 25 </action> | |
| 26 --> | |
| 27 | |
| 28 <action type="shell_command">echo "[DEBUG] AFTER:" && pwd</action> | |
| 29 <action type="shell_command">echo "[DEBUG] DIR LISTING:" && ls -l</action> | |
| 30 | |
| 31 <action type="set_environment_for_install"> | |
| 32 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/"> | |
| 33 <package name="R" version="3.0.3" /> | |
| 34 </repository> | |
| 35 </action> | |
| 36 <action type="set_environment"> | |
| 37 <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable> | |
| 38 </action> | |
| 39 <action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action> | |
| 40 | |
| 41 <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action> | |
| 42 | |
| 43 <action type="shell_command">echo "[DEBUG] WORKING DIR:" && pwd</action> | |
| 44 <action type="shell_command">echo "[DEBUG] DIR LISTING:" && ls -l</action> | |
| 45 | |
| 46 <action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action> | |
| 47 <!-- | |
| 48 <action type="shell_command">export R_LIBS=$INSTALL_DIR && R CMD INSTALL --> <!--build QDNAseq_1.0.5.tar.gz</action> | |
| 49 --> | |
| 50 <!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>--> | |
| 51 </actions> | |
| 52 </install> | |
| 53 | |
| 54 <readme> | |
| 55 Should install QDNAseq package from bioconductor. | |
| 56 </readme> | |
| 57 </package> | |
| 58 | |
| 59 </tool_dependency> |