Mercurial > repos > lomereiter > sambamba_filter
diff readme.txt @ 2:930c9fd5eeab
Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
| author | lparsons |
|---|---|
| date | Wed, 24 Jul 2013 13:32:24 -0400 |
| parents | |
| children | f81259dcaea7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Wed Jul 24 13:32:24 2013 -0400 @@ -0,0 +1,14 @@ +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.