| Port details |
- pbbam PacBio BAM C++ library, with SWIG bindings
- 0.18.0_9 biology
 =2      0.18.0_8Version of this port present on the latest quarterly branch. - There is no maintainer for this port.
- Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
- Port Added: 2018-04-23 16:08:32
- Last Update: 2024-10-03 10:25:14
- Commit Hash: 55cfbcf
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSD3CLAUSE
- WWW:
- https://github.com/PacificBiosciences/pbbam
- Description:
- As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry
standard BAM format for (both aligned and unaligned) basecall data files. We
have also formulated a BAM companion file format (bam.pbi) enabling fast access
to a richer set of per-read information as well as compatibility for software
built around the legacy cmp.h5 format.
The pbbam software package provides components to create, query, & edit PacBio
BAM files and associated indices. These components include a core C++ library,
bindings for additional languages, and command-line utilities.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/pbbam/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/pbbam
- pkg install pbbam
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: pbbam
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1550453627
SHA256 (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a
SIZE (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 8136503
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- meson : devel/meson
- ninja : devel/ninja
- pkgconf>=1.3.0_1 : devel/pkgconf
- python3.11 : lang/python311
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- python3.11 : lang/python311
- Library dependencies:
-
- libhts.so : biology/htslib
- libboost_regex.so : devel/boost-libs
- This port is required by:
- for Libraries
-
Deleted ports which required this port:
- * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options:- No options to configure
- Options name:
- biology_pbbam
- USES:
- compiler:c++14-lang localbase meson pkgconfig python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.18.0_9
03 Oct 2024 10:25:14
 |
Dima Panov (fluffy) |
*/*: bump consumers after devel/boost* update
With hat: office
Sponsored by: Future Crew, LLC |
0.18.0_8
06 Jan 2023 01:25:09
|
Jason W. Bacon (jwb) |
biology/pbbam: Bump PORTREVISION for biology/htslib update |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
0.18.0_7
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
0.18.0_7
12 Aug 2022 14:46:53
|
Dima Panov (fluffy) |
*/*: bump all consumers after recent boost upgrade |
0.18.0_6
22 May 2022 20:17:16
|
Dima Panov (fluffy) |
devel/boost-all: bump all library consumers after boost upgrade
PR: 246106 |
0.18.0_5
16 Oct 2021 09:51:39
|
Jimmy Olgeni (olgeni) |
*: fix tab vs. space issues, and comments according to the guide. |
0.18.0_5
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.18.0_5
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.18.0_5
03 Aug 2020 17:40:04
 |
jwb |
biology/htslib: Upgrade to 1.10.2
Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags
Bump PORTREVISION on dependents that don't require additional patching
PR: 248089 |
0.18.0_4
11 Dec 2019 17:53:49
|
jbeich |
devel/boost-*: update to 1.72.0
Changes: http://www.boost.org/users/history/version_1_72_0.html
PR: 241449
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D22136 |
0.18.0_3
24 Nov 2019 15:53:01
|
jwb |
biology/unanimity and dependencies: Flag as no longer open source
PacBio now provides unanimity only as a binary package through bioconda.
See https://github.com/PacificBiosciences/ccs. |
0.18.0_3
19 Aug 2019 15:35:28
|
jbeich |
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 |
0.18.0_2
26 Jul 2019 20:46:57
|
gerald |
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 |
0.18.0_1
12 Apr 2019 06:36:31
|
jbeich |
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 |
0.18.0
19 Feb 2019 23:03:41
|
jwb |
biology/pbbam: Upgrade to 0.18.0 release
In preparation for unanimity upgrade |
g20180416_3
12 Dec 2018 01:35:36
|
gerald |
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 |
g20180416_2
12 Dec 2018 00:15:50
|
jbeich |
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 |
g20180416_1
18 Sep 2018 08:14:23
|
linimon |
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) |
g20180416_1
09 Aug 2018 06:58:31
|
jbeich |
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 |
g20180416
23 Apr 2018 16:08:21
|
jwb |
biology/pbbam: PacBio BAM C++ library, with SWIG bindings
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15154 |
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