Mercurial > repos > yhoogstrate > edger_with_design_matrix
diff tool_dependencies.xml @ 1:a4a4c88783ea draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
| author | yhoogstrate |
|---|---|
| date | Tue, 01 Sep 2015 04:59:05 -0400 |
| parents | acb56603b268 |
| children | ec951a5017f8 |
line wrap: on
line diff
--- a/tool_dependencies.xml Mon Aug 31 11:00:02 2015 -0400 +++ b/tool_dependencies.xml Tue Sep 01 04:59:05 2015 -0400 @@ -1,60 +1,36 @@ <?xml version="1.0"?> <tool_dependency> - <package name="R" version="3.0.3"> - <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="biocLite_edgeR_limma" version="latest"> - <install version="1.0"> - <actions> - <action type="set_environment_for_install"> - <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="R" version="3.0.3" /> - </repository> - - </action> - <action type="make_directory">$INSTALL_DIR</action> - <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> - </actions> - </install> - <readme> - Installs the latest bioc packages: edgeR & Limma - </readme> - </package> - - <package name="design_matrix_creator" version="1.0.0"> - <install version="1.0"> - <actions> - <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - </package> - - <package name="edger_dge_table_to_bedgraph" version="1.0.0"> - <install version="1.0"> - <actions> - <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - </package> + <package name="edger" version="3.11.0"> + <repository changeset_revision="8b2965eeb34e" name="package_r_edger_3_11_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="design_matrix_creator" version="1.0.0"> + <install version="1.0"> + <actions> + <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/design_matrix_creator $INSTALL_DIR/bin/</action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> + + <package name="edger_dge_table_to_bedgraph" version="1.0.0"> + <install version="1.0"> + <actions> + <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> </tool_dependency>