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test-nginx01 & pg02
Port details
jellyfish Fast, memory-efficient counting of k-mers in DNA
2.2.6_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 24 Mar 2016 13:53:24
License: GPLv3+
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.

WWW: http://www.genome.umd.edu/jellyfish.html
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (60 items)
  1. /usr/local/share/licenses/jellyfish-2.2.6_2/catalog.mk
  2. /usr/local/share/licenses/jellyfish-2.2.6_2/LICENSE
  3. /usr/local/share/licenses/jellyfish-2.2.6_2/GPLv3+
  4. bin/jellyfish
  5. include/jellyfish-2.2.6/jellyfish/allocators_mmap.hpp
  6. include/jellyfish-2.2.6/jellyfish/atomic_bits_array.hpp
  7. include/jellyfish-2.2.6/jellyfish/atomic_field.hpp
  8. include/jellyfish-2.2.6/jellyfish/atomic_gcc.hpp
  9. include/jellyfish-2.2.6/jellyfish/backtrace.hpp
  10. include/jellyfish-2.2.6/jellyfish/binary_dumper.hpp
  11. include/jellyfish-2.2.6/jellyfish/bloom_common.hpp
  12. include/jellyfish-2.2.6/jellyfish/bloom_counter2.hpp
  13. include/jellyfish-2.2.6/jellyfish/bloom_filter.hpp
  14. include/jellyfish-2.2.6/jellyfish/circular_buffer.hpp
  15. include/jellyfish-2.2.6/jellyfish/compare_and_swap.hpp
  16. include/jellyfish-2.2.6/jellyfish/cooperative_pool.hpp
  17. include/jellyfish-2.2.6/jellyfish/cooperative_pool2.hpp
  18. include/jellyfish-2.2.6/jellyfish/cpp_array.hpp
  19. include/jellyfish-2.2.6/jellyfish/divisor.hpp
  20. include/jellyfish-2.2.6/jellyfish/dumper.hpp
  21. include/jellyfish-2.2.6/jellyfish/err.hpp
  22. include/jellyfish-2.2.6/jellyfish/file_header.hpp
  23. include/jellyfish-2.2.6/jellyfish/generator_manager.hpp
  24. include/jellyfish-2.2.6/jellyfish/generic_file_header.hpp
  25. include/jellyfish-2.2.6/jellyfish/hash_counter.hpp
  26. include/jellyfish-2.2.6/jellyfish/int128.hpp
  27. include/jellyfish-2.2.6/jellyfish/jellyfish.hpp
  28. include/jellyfish-2.2.6/jellyfish/json.h
  29. include/jellyfish-2.2.6/jellyfish/large_hash_array.hpp
  30. include/jellyfish-2.2.6/jellyfish/large_hash_iterator.hpp
  31. include/jellyfish-2.2.6/jellyfish/locks_pthread.hpp
  32. include/jellyfish-2.2.6/jellyfish/mapped_file.hpp
  33. include/jellyfish-2.2.6/jellyfish/mer_dna.hpp
  34. include/jellyfish-2.2.6/jellyfish/mer_dna_bloom_counter.hpp
  35. include/jellyfish-2.2.6/jellyfish/mer_heap.hpp
  36. include/jellyfish-2.2.6/jellyfish/mer_iterator.hpp
  37. include/jellyfish-2.2.6/jellyfish/mer_overlap_sequence_parser.hpp
  38. include/jellyfish-2.2.6/jellyfish/mer_qual_iterator.hpp
  39. include/jellyfish-2.2.6/jellyfish/misc.hpp
  40. include/jellyfish-2.2.6/jellyfish/offsets_key_value.hpp
  41. include/jellyfish-2.2.6/jellyfish/rectangular_binary_matrix.hpp
  42. include/jellyfish-2.2.6/jellyfish/simple_circular_buffer.hpp
  43. include/jellyfish-2.2.6/jellyfish/sorted_dumper.hpp
  44. include/jellyfish-2.2.6/jellyfish/stdio_filebuf.hpp
  45. include/jellyfish-2.2.6/jellyfish/storage.hpp
  46. include/jellyfish-2.2.6/jellyfish/stream_iterator.hpp
  47. include/jellyfish-2.2.6/jellyfish/stream_manager.hpp
  48. include/jellyfish-2.2.6/jellyfish/text_dumper.hpp
  49. include/jellyfish-2.2.6/jellyfish/thread_exec.hpp
  50. include/jellyfish-2.2.6/jellyfish/time.hpp
  51. include/jellyfish-2.2.6/jellyfish/token_ring.hpp
  52. include/jellyfish-2.2.6/jellyfish/whole_sequence_parser.hpp
  53. lib/libjellyfish-2.0.a
  54. lib/libjellyfish-2.0.so
  55. lib/libjellyfish-2.0.so.2
  56. lib/libjellyfish-2.0.so.2.0.0
  57. libdata/pkgconfig/jellyfish-2.0.pc
  58. man/man1/jellyfish.1.gz
  59. @postexec /sbin/ldconfig -m /usr/local/lib
  60. @postunexec /sbin/ldconfig -R
  61. Collapse this list.

To install the port: cd /usr/ports/biology/jellyfish/ && make install clean
To add the package: pkg install jellyfish

PKGNAME: jellyfish

distinfo:

TIMESTAMP = 1482069678
SHA256 (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 800bc60aaec273dc04296ee7493e714457f2fe88551f76693e5d9f9a679dd35e
SIZE (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 660858


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. yaggo : devel/yaggo
  2. autoconf-2.69 : devel/autoconf
  3. autoheader-2.69 : devel/autoconf
  4. autoreconf-2.69 : devel/autoconf
  5. aclocal-1.15 : devel/automake
  6. automake-1.15 : devel/automake
  7. libtoolize : devel/libtool
  8. gmake : devel/gmake
  9. pkgconf>=1.3.0_1 : devel/pkgconf
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
autoreconf compiler:c++11-lib gmake libtool pathfix pkgconfig

Master Sites:
  1. https://codeload.github.com/gmarcais/Jellyfish/tar.gz/v2.2.6?dummy=/

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
31 Jan 2018 01:07:08
Original commit files touched by this commit  2.2.6_2
Revision:460452
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
10 Sep 2017 20:55:39
Original commit files touched by this commit  2.2.6_2
Revision:449591
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
01 Apr 2017 15:23:32
Original commit files touched by this commit  2.2.6_1
Revision:437439
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
01 Jan 2017 03:45:13
Original commit files touched by this commit  2.2.6
Revision:430235
sunpoet search for other commits by this committer
Remove BROKEN_FreeBSD_9

Approved by:	portmgr (blanket)
19 Dec 2016 16:52:34
Original commit files touched by this commit  2.2.6
Revision:428954
jrm search for other commits by this committer
biology/jellyfish: Update to version 2.2.6

Upstream changes since version 2.2.4:
- Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1).
- Fix bug in parsing function that made it stop on sequences that consist
  of only empty lines.
- New methods in bindings to enumerate the mers of a string.

Approved by:	AMDmi3 (mentor)
Differential Revision:	https://reviews.freebsd.org/D8204
11 Nov 2016 09:31:03
Original commit files touched by this commit  2.2.4
Revision:425879
linimon search for other commits by this committer
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.

Approved by:	portmgr (tier-2 blanket)
21 Oct 2016 15:21:13
Original commit files touched by this commit  2.2.4
Revision:424427
mat search for other commits by this committer
Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093
01 Apr 2016 13:29:17
Original commit files touched by this commit  2.2.4
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
29 Mar 2016 20:55:49
Original commit files touched by this commit  2.2.4
Revision:412137
amdmi3 search for other commits by this committer
- Use more appropriate BROKEN instead of IGNORE

PR:		208367
Submitted by:	bacon4000@gmail.com (maintainer)
Suggested by:	rakuco
24 Mar 2016 13:53:06
Original commit files touched by this commit  2.2.4
Revision:411785
amdmi3 search for other commits by this committer
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.

WWW: http://www.genome.umd.edu/jellyfish.html

PR:		207929
Submitted by:	bacon4000@gmail.com

Number of commits found: 10

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