Mercurial > repos > bebatut > sortmerna
diff tool_dependencies.xml @ 15:baab049d3aff draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
| author | bebatut |
|---|---|
| date | Wed, 10 Feb 2016 04:02:18 -0500 |
| parents | 011ec5258e71 |
| children |
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--- a/tool_dependencies.xml Wed Nov 18 09:19:17 2015 -0500 +++ b/tool_dependencies.xml Wed Feb 10 04:02:18 2016 -0500 @@ -5,43 +5,55 @@ <actions_group> <actions architecture="x86_64" os="linux"> <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> - <action type="autoconf"/> + <action type="shell_command"><![CDATA[ + ./build.sh --prefix=$INSTALL_DIR + ]]> + </action> <action type="change_directory">../</action> - <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action> + <action type="make_directory">$INSTALL_DIR/bin/</action> + <action type="move_file"> + <source>sortmerna-2.0/sortmerna</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>sortmerna-2.0/indexdb_rna</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action> <action type="move_directory_files"> - <source_directory>sortmerna-2.0/</source_directory> - <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory> + <source_directory>sortmerna-2.0/rRNA_databases/</source_directory> + <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory> </action> <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable> + <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> <actions architecture="x86_64" os="darwin"> <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> <action type="shell_command"><![CDATA[ - export CC=clang && export CXX=clang++ && ./configure && make && make install + export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install ]]> </action> <action type="change_directory">../</action> - <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action> + <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action> <action type="move_directory_files"> - <source_directory>sortmerna-2.0/</source_directory> - <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory> + <source_directory>sortmerna-2.0/rRNA_databases/</source_directory> + <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory> </action> <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable> + <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </actions_group> </install> <readme> - SortMeRNA requires g++ 4.3 or later. + SortMeRNA requires g++ 4.8 or later. Note: the Clang compiler on Mac (distributed through Xcode) does not support multithreading. The user is recommended to install the original GCC compiler via MacPorts </readme> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency>