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bowtie2-2.3.5.1-lp152.2.1 RPM for aarch64

From OpenSuSE Ports Leap 15.2 for aarch64

Name: bowtie2 Distribution: openSUSE Leap 15.2
Version: 2.3.5.1 Vendor: openSUSE
Release: lp152.2.1 Build date: Thu May 14 07:11:46 2020
Group: Productivity/Scientific/Other Build host: obs-arm-2
Size: 3530289 Source RPM: bowtie2-2.3.5.1-lp152.2.1.src.rpm
Packager: https://bugs.opensuse.org
Url: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Summary: Fast and memory-efficient short read aligner
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing
reads to long reference sequences. It is particularly good at aligning
reads of about 50 up to 100s or 1,000s of characters, and particularly good
at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes
the genome with an FM Index to keep its memory footprint small: for the
human genome, its memory footprint is typically around 3.2 GB. Bowtie 2
supports gapped, local, and paired-end alignment modes.

Provides

Requires

License

GPL-3.0-only

Changelog

* Tue May 12 2020 Guillaume GARDET <guillaume.gardet@opensuse.org>
  - Fix aarch64 build with:
    * simde sources
    * export POPCNT_CAPABILITY=0
* Sat Nov 30 2019 Atri Bhattacharya <badshah400@gmail.com>
  - Use %%license to install LICENSE file.
* Thu Nov 07 2019 Atri Bhattacharya <badshah400@gmail.com>
  - Update to version 2.3.5.1:
    * Added official support for BAM input files.
    * Added official support for CMake build system.
    * Added changes to Makefile for creating Reproducible builds
      [gh#BenLangmead/bowtie2#210].
    * Fix an issue whereby building on aarch64 would require
      patching sed commands [gh#BenLangmead/bowtie2#243].
    * Fix an issue whereby `bowtie2` would incorrectly throw an
      error while processing `--interleaved` input.
  - Changes from version 2.3.5:
    * Added support for obtaining input reads directly from the
      Sequence Read Archive, via NCBI's [NGS language
      bindings](https://github.com/ncbi/ngs).  This is activated via
      the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc)
      option.  This implementation is based on Daehwan Kim's in
      [HISAT2](https://ccb.jhu.edu/software/hisat2).  Supports both
      unpaired and paired-end inputs.
    * Bowtie 2 now compiles on ARM architectures (via
      [gh#BenLangmead/bowtie2#216].
    * `--interleaved` can now be combined with FASTA inputs (worked
      only with FASTQ before).
    * Fixed issue whereby large indexes were not successfully found
      in the `$BOWTIE2_INDEXES` directory.
    * Fixed input from FIFOs (e.g. via process substitution) to
      distinguish gzip-compressed versus uncompressed input.
    * Fixed issue whereby arguments containing `bz2` `lz4` were
      misinterpretted as files.
    * Fixed several compiler warnings.
    * Fixed issue whereby both ends of a paired-end read could have
      negative TLEN if they exactly coincided
    * Fixed issue whereby `bowtie2-build` would hang on end-of-file
      [gh#BenLangmead/bowtie2#228].
    * Fixed issue whereby wrapper script would sometimes create
      zombie processes [gh#BenLangmead/bowtie2#51].
    * Fixed issue whereby `bowtie2-build` and `bowtie2-inspect`
      wrappers would fail on some versions of Python/PyPy.
    * Replaced old, unhelpful `README.md` in the project with a
      version that includes badges, links and some highlights from
      the manual.
* Wed Feb 28 2018 badshah400@gmail.com
  - Update to version 2.3.4.1:
    * Fixed an issue with --reorder that caused bowtie2 to crash
      while reordering SAM output
  - Changes from version 2.3.4:
    * Fixed major issue causing corrupt SAM output when using many
      threads (-p/--threads) on certain systems.
    * Fixed an issue whereby bowtie2 processes could overwrite each
      others' named pipes on HPC systems.
    * Fixed an issue causing bowtie2-build and bowtie2-inspect to
      return prematurely on Windows.
    * Fixed issues raised by compiler "sanitizers" that could
      potentially have caused memory corruption or undefined
      behavior.
    * Added the "continuous FASTA" input format (-F) for aligning
      all the k-mers in the sequences of a FASTA file. Useful for
      determining mapability of regions of the genome, and similar
      tasks.
  - Run sed on binaries to modify env based hashbangs to ones that
    directly call executables.
  - Drop bowtie2-gcc6.patch; incorporated upstream.
* Mon Sep 04 2017 mpluskal@suse.com
  - Update to version 2.3.2:
    * Added support for interleaved paired-end FASTQ inputs
      (--interleaved)
    * Now reports MREVERSE SAM flag for unaligned end when only one
      end of a pair aligns
    * Fixed issue where first character of some read names was
      omitted from SAM output when using tabbed input formats.
    * Added --sam-no-qname-trunc option.
    * Fixed compilation error caused by pointer comparison issue in aligner_result.cpp
    * Removed termcap and readline dependencies introduced in v2.3.1
    * Fixed compilation issues caused by gzbuffer function when
      compiling with zlib v1.2.3.5 and earlier.
    * Fixed issue that would cause Bowtie 2 hang when aligning FASTA
      inputs with more than one thread
  - Changes for version 2.3.0:
    * Code related to read parsing was completely rewritten to improve
      scalability to many threads.
    * TBB is now the default threading library.
    * Bowtie now uses a queue-based lock rather than a spin or
      heavyweight lock.
    * Unnecessary thread synchronization removed
    * Fixed issue with parsing FASTA records with greater-than symbol
      in the name
    * Changed default for --bmaxdivn to yield better memory footprint
      and running time when building an index with many threads
  - Add bowtie2-gcc6.patch (fixes compilation with gcc6+)
  - Build using optflags
  - Update download url
  - Small package cleanup with spec-cleaner
* Thu May 05 2016 flyos@mailoo.org
  - Initial release

Files

/usr/bin/bowtie2
/usr/bin/bowtie2-align-l
/usr/bin/bowtie2-align-s
/usr/bin/bowtie2-build
/usr/bin/bowtie2-build-l
/usr/bin/bowtie2-build-s
/usr/bin/bowtie2-inspect
/usr/bin/bowtie2-inspect-l
/usr/bin/bowtie2-inspect-s
/usr/share/doc/packages/bowtie2
/usr/share/doc/packages/bowtie2/AUTHORS
/usr/share/doc/packages/bowtie2/MANUAL
/usr/share/doc/packages/bowtie2/NEWS
/usr/share/doc/packages/bowtie2/TUTORIAL
/usr/share/doc/packages/bowtie2/VERSION
/usr/share/licenses/bowtie2
/usr/share/licenses/bowtie2/LICENSE


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Fabrice Bellet, Sat Mar 9 12:07:01 2024