Mercurial > repos > lomereiter > sambamba_filter
diff tool_dependencies.xml @ 5:123168c85390
updated to 0.4.7; use precompiled binaries
author | lomereiter <lomereiter@gmail.com> |
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date | Tue, 04 Nov 2014 18:34:37 +0300 |
parents | 930c9fd5eeab |
children | af897e0a3c13 |
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--- a/tool_dependencies.xml Wed Jul 24 13:33:50 2013 -0400 +++ b/tool_dependencies.xml Tue Nov 04 18:34:37 2014 +0300 @@ -1,36 +1,33 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sambamba" version="0.3.3"> - <install version="1.0"> - <actions> - <action type="shell_command">git clone --recursive https://github.com/lomereiter/sambamba</action> - <action type="shell_command">git checkout v0.3.3</action> - <action type="shell_command">git submodule update --recursive</action> - <action type="shell_command">make release</action> - <action type="move_directory_files"> - <source_directory>build</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file. - -There are a three options for installation of sambamba: - - 1) Automated toolshed installation. This requires that a D2 compiler (dmd >= 2.063) is installed. The automated installation will attempt to use the dmd compiler and thus **will not be optimized**. - - 2) Manual compilation. For performance reasons, the sambamba developers recommend you use either GDC or LDC as they use GCC and LLVM backends and do a much better job at optimization. You should then use the sambamba-ldmd2-64 make target. See https://github.com/lomereiter/sambamba/wiki/Command-line-tools for more information. - - 3) Precompiled binary (recommended). You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba. - -If you choose option 2 or 3, sambamba may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir". See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. - -The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper. -The sambamba development repository is at: https://github.com/lomereiter/sambamba. - </readme> - </package> + <package name="sambamba" version="0.4.7"> + <install version="1.0"> + <actions_group> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url"> + https://github.com/lomereiter/sambamba/releases/download/v0.4.7/sambamba_v0.4.7_osx.tar.bz2 + </action> + <action type="move_file"> + <source>sambamba_v0.4.7</source> + <destination>$INSTALL_DIR/bin/sambamba</destination> + </action> + </actions> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url"> + https://github.com/lomereiter/sambamba/releases/download/v0.4.7/sambamba_v0.4.7_centos5.tar.bz2 + </action> + <action type="move_file"> + <source>sambamba_v0.4.7</source> + <destination>$INSTALL_DIR/bin/sambamba</destination> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme> + Downloads the precompiled 64bit Linux or Mac OS X binaries from the official repository 'Releases' section. + </readme> + </package> </tool_dependency>