Mercurial > repos > lomereiter > sambamba_filter
annotate readme.txt @ 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 | 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.
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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. |
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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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2 |
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Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
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3 There are a three options for installation of sambamba: |
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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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4 |
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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6 |
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.
lparsons
parents:
diff
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8 |
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.
lparsons
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10 |
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.
lparsons
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12 |
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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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. |