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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
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children f81259dcaea7
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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1 This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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3 There are a three options for installation of sambamba:
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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5 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**.
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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7 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.
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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9 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.
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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11 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.
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
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930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
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13 The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper
930c9fd5eeab Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
lparsons
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14 The sambamba development repository is at: https://github.com/lomereiter/sambamba.