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Port details
unanimity Pacific Biosciences consensus library and applications
3.4.1_3 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 3.4.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-24 14:17:02
Last Update: 2019-08-19 16:35:28
SVN Revision: 509290
License: BSD3CLAUSE
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (87 items)
  1. /usr/local/share/licenses/unanimity-3.4.1_3/catalog.mk
  2. /usr/local/share/licenses/unanimity-3.4.1_3/LICENSE
  3. /usr/local/share/licenses/unanimity-3.4.1_3/BSD3CLAUSE
  4. bin/ChimeraLabeler
  5. bin/arrow
  6. bin/ccs
  7. bin/ccs_sim
  8. bin/gcpp
  9. bin/genomic_sim
  10. bin/variantCaller
  11. include/pacbio/UnanimityConfig.h
  12. include/pacbio/UnanimityVersion.h
  13. include/pacbio/align/AffineAlignment.h
  14. include/pacbio/align/AlignConfig.h
  15. include/pacbio/align/BandedAligner.h
  16. include/pacbio/align/BandedChainAlignment.h
  17. include/pacbio/align/ChainScorer.h
  18. include/pacbio/align/ChainSeeds.h
  19. include/pacbio/align/ChainSeedsConfig.h
  20. include/pacbio/align/FilterSeeds.h
  21. include/pacbio/align/FindSeeds.h
  22. include/pacbio/align/FindSeedsConfig.h
  23. include/pacbio/align/HomopolymerHasher.h
  24. include/pacbio/align/LinearAlignment.h
  25. include/pacbio/align/LocalAlignment.h
  26. include/pacbio/align/PairwiseAlignment.h
  27. include/pacbio/align/SeedScorer.h
  28. include/pacbio/align/SparseAlignment.h
  29. include/pacbio/align/internal/BCAlignBlocks.h
  30. include/pacbio/align/internal/BCAlignImpl.h
  31. include/pacbio/ccs/Consensus.h
  32. include/pacbio/ccs/ConsensusSettings.h
  33. include/pacbio/ccs/SparseAlignment.h
  34. include/pacbio/ccs/Whitelist.h
  35. include/pacbio/chimera/ChimeraLabel.h
  36. include/pacbio/chimera/ChimeraLabeler.h
  37. include/pacbio/chimera/ChimeraResultWriter.h
  38. include/pacbio/consensus/AbstractMatrix.h
  39. include/pacbio/consensus/Coverage.h
  40. include/pacbio/consensus/EasyReadScorer.h
  41. include/pacbio/consensus/Evaluator.h
  42. include/pacbio/consensus/Integrator.h
  43. include/pacbio/consensus/IntervalMask.h
  44. include/pacbio/consensus/MatrixViewConvention.h
  45. include/pacbio/consensus/ModelConfig.h
  46. include/pacbio/consensus/ModelSelection.h
  47. include/pacbio/consensus/Mutation.h
  48. include/pacbio/consensus/Polish.h
  49. include/pacbio/consensus/PolishResult.h
  50. include/pacbio/consensus/Template.h
  51. include/pacbio/consensus/internal/ModelInternalInitializer.h
  52. include/pacbio/data/ChemistryMapping.h
  53. include/pacbio/data/ChemistryTriple.h
  54. include/pacbio/data/Interval.h
  55. include/pacbio/data/IntervalTree.h
  56. include/pacbio/data/PlainOption.h
  57. include/pacbio/data/Read.h
  58. include/pacbio/data/ReadId.h
  59. include/pacbio/data/Sequence.h
  60. include/pacbio/data/State.h
  61. include/pacbio/data/StrandType.h
  62. include/pacbio/data/SubreadResultCounter.h
  63. include/pacbio/data/internal/BaseEncoding.h
  64. include/pacbio/data/internal/ConversionFunctions.h
  65. include/pacbio/denovo/PoaConsensus.h
  66. include/pacbio/denovo/PoaGraph.h
  67. include/pacbio/denovo/RangeFinder.h
  68. include/pacbio/denovo/SparsePoa.h
  69. include/pacbio/exception/CCSExceptions.h
  70. include/pacbio/exception/InvalidEvaluatorException.h
  71. include/pacbio/exception/ModelError.h
  72. include/pacbio/exception/StateError.h
  73. include/pacbio/io/Utility.h
  74. include/pacbio/parallel/WorkQueue.h
  75. include/pacbio/util/ExecUtils.h
  76. include/pacbio/util/Timer.h
  77. lib/libunanimity.so
  78. lib/libunanimity.so.3
  79. lib/libunanimity.so.3.0
  80. lib/libunanimity.so.3.0.0
  81. lib/python2.7/site-packages/ConsensusCore2.py
  82. lib/python2.7/site-packages/ConsensusCore2.pyc
  83. lib/python2.7/site-packages/ConsensusCore2.pyo
  84. lib/python2.7/site-packages/_ConsensusCore2.so
  85. libdata/pkgconfig/unanimity.pc
  86. @postexec /usr/sbin/service ldconfig restart > /dev/null
  87. @postunexec /usr/sbin/service ldconfig restart > /dev/null
Collapse this list.
Dependency lines:
  • unanimity>0:biology/unanimity
To install the port: cd /usr/ports/biology/unanimity/ && make install clean
To add the package: pkg install unanimity
PKGNAME: unanimity
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. seqan>=2.4.0 : biology/seqan
  2. swig30>=3.0 : devel/swig30
  3. py27-numpy>0 : math/py-numpy@py27
  4. meson : devel/meson
  5. ninja : devel/ninja
  6. pkgconf>=1.3.0_1 : devel/pkgconf
  7. python2.7 : lang/python27
Runtime dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. python2.7 : lang/python27
Library dependencies:
  1. libhts.so : biology/htslib
  2. libboost_regex.so : devel/boost-libs
  3. libpbbam.so.0.18.0 : biology/pbbam
  4. libpbcopper.so.0.4.1 : biology/pbcopper
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Aug 2019 15:35:28
Original commit files touched by this commit  3.4.1_3
Revision:509290
jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
26 Jul 2019 20:46:57
Original commit files touched by this commit  3.4.1_2
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
25 Apr 2019 13:25:50
Original commit files touched by this commit  3.4.1_1
Revision:499993
antoine search for other commits by this committer
Clean up plist
12 Apr 2019 06:36:31
Original commit files touched by this commit  3.4.1_1
Revision:498698
jbeich search for other commits by this committer
devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303
24 Feb 2019 16:04:58
Original commit files touched by this commit  3.4.1
Revision:493769
jwb search for other commits by this committer
biology/unanimity: Upgrade to 3.4.1

Minor fixes and enhancements upstream.
22 Feb 2019 23:26:02
Original commit files touched by this commit  3.4.0
Revision:493621
antoine search for other commits by this committer
biology/unanimity is not compatible with python 3.x

PR:		234633
20 Feb 2019 01:36:51
Original commit files touched by this commit  3.4.0
Revision:493402
jwb search for other commits by this committer
biology/unanimity: Upgrade to 3.4.0

Switch from cmake to new meson build system
Tests disabled for now pending work on unbundling googletest
25 Dec 2018 20:25:40
Original commit files touched by this commit  3.1.0_2
Revision:488341
tcberner search for other commits by this committer
Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine
12 Dec 2018 01:35:36
Original commit files touched by this commit  3.1.0_2
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 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, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
12 Dec 2018 00:15:50
Original commit files touched by this commit  3.1.0_1
Revision:487266
jbeich search for other commits by this committer
devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645
18 Sep 2018 08:14:23
Original commit files touched by this commit  3.1.0
Revision:479990
linimon search for other commits by this committer
More precisely specify USES=compiler to fix build on gcc-based
platforms such as powerpc64.

Tested on powerpc64, amd64.

Approved by:	portmgr (tier-2 blanket)
25 Aug 2018 22:54:54
Original commit files touched by this commit  3.1.0
Revision:478089
jwb search for other commits by this committer
biology/unanimity: Upgrade to latest release, soften dep version requirements

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16902
09 Aug 2018 06:58:31
Original commit files touched by this commit  g20180307_1
Revision:476723
jbeich search for other commits by this committer
devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165
22 Jun 2018 00:03:08
Original commit files touched by this commit  g20180307
Revision:473010
linimon search for other commits by this committer
Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
24 Apr 2018 14:16:46
Original commit files touched by this commit  g20180307
Revision:468214
jwb search for other commits by this committer
biology/unanimity: Pacific Biosciences consensus library and applications

Reviewed by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15172

Number of commits found: 15

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