| Port details |
- canu Single molecule sequence assembler
- 2.2_2 biology
 =0      Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2017-12-22 01:30:37
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- Also Listed In: java perl5
- License: GPLv2
- Description:
- Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Canu is a hierarchical assembly pipeline which runs in four steps:
Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences
  ¦  ¦  ¦  ¦  - pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/canu/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/canu
- pkg install canu
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: canu
- Flavors: there is no flavor information for this port.
- NOT_FOR_ARCHS: armv6 armv7 i386 mips powerpc powerpcspe
- distinfo:
- TIMESTAMP = 1639774550
SHA256 (canu-2.2.tar.xz) = e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404
SIZE (canu-2.2.tar.xz) = 2400192
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:
-
- gmake>=4.3 : devel/gmake
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Runtime dependencies:
-
- gnuplot : math/gnuplot
- java : java/openjdk8
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Library dependencies:
-
- libboost_regex.so : devel/boost-libs
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_canu
- USES:
- compiler:c++11-lang gmake localbase perl5 tar:xz
- 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 |
|---|
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) |
2.2_2
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  ) |
2.2_2
12 Aug 2022 14:46:53
|
Dima Panov (fluffy) |
*/*: bump all consumers after recent boost upgrade |
2.2_1
22 May 2022 20:17:16
|
Dima Panov (fluffy) |
devel/boost-all: bump all library consumers after boost upgrade
PR: 246106 |
2.2
20 Dec 2021 12:59:13
|
Antoine Brodin (antoine) |
biology/canu: fix CATEGORIES |
2.2
19 Dec 2021 21:06:56
|
Jason W. Bacon (jwb) |
biology/canu: Update to 2.2
FreeBSD port: Add support for aarch64 and powerpc64 using simde
Not yet supported upstream
Several upstream bug fixes and minor enhancements since 2.1
Changes: https://github.com/marbl/canu/tags |
2.1_1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.1_1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.1_1
11 Jan 2021 16:51:16
 |
jwb |
biology/canu: Drop dependency on gcc
Replace compiler:openmp with compiler:c++11-lang and localbase
PR: port/247753, ports/252379 |
2.1
14 Sep 2020 22:27:37
|
jwb |
biology/canu: Upgrade to 2.1
Numerous functional improvements for ease of use and output quality
A few bug fixes
Reported by: portscout |
2.0
17 May 2020 02:25:17
|
linimon |
Mark as BROKEN on powerpc64:
utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error:
'get_deleter' declared as a 'virtual' field
This may have something to do with compiler:openmp in USES. However,
it has broken for more than 6 months at this point.
Approved by: portmgr (tier-2 blanket) |
2.0
20 Mar 2020 18:14:24
|
jwb |
biology/canu: Upgrade to 2.0
Several routine enhancements and bug fixes
Reported by: portscout |
1.9_1
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 |
1.9
08 Nov 2019 14:03:15
|
jwb |
biology/canu: Upgrade to 1.9
Numerous bug fixes and enhancements
Reported by: portscout |
1.8_5
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 |
1.8_4
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 |
1.8_3
25 Jul 2019 09:02:20
|
amdmi3 |
- Update WWW
Approved by: portmgr blanket |
1.8_3
18 Apr 2019 12:15:56
|
jwb |
biology/canu: Fix build on powerpc64 and aarch64
Should also work on powerpc and arm*, but unable to test
PR: 237105
Reported by: pkubaj |
1.8_3
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 |
1.8_2
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 |
1.8_1
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 |
1.8
04 Nov 2018 14:29:03
|
jwb |
biology/canu: Upgrade to 1.8, add experimental SLURM integration
Solves build issue with gcc8.
PR: 232930
Reported by: gerald
Approved by: jrm (mentor, implicit) |
1.7_2
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 |
1.7_1
29 Jul 2018 22:18:46
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.
This includes ports
- featuring USE_GCC=yes or USE_GCC=any,
- featuring USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and those
- with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.
PR: 222542 |
1.7
21 Jun 2018 23:52:37
|
linimon |
Mark as broken on aarch64, and, where appropriate, armvX.
While here, pet portlint.
Approved by: portmgr (tier-2 blanket) |
1.7
26 Apr 2018 04:16:15
|
jwb |
biology/canu: Upgrade to 1.7 release
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15201 |
1.6_3
18 Apr 2018 13:57:43
|
jbeich |
devel/boost-*: update to 1.67.0
Changes: http://www.boost.org/users/history/version_1_67_0.html
PR: 227427
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D15030 |
1.6_2
10 Mar 2018 17:46:06
|
gerald |
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079). |
1.6_1
18 Jan 2018 04:11:03
|
jbeich |
devel/boost-*: update to 1.66.0
Changes: http://www.boost.org/users/history/version_1_66_0.html
PR: 223922
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D13279 |
1.6
22 Dec 2017 14:14:11
|
jwb |
biology/canu: Replace += with = for depends
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D13574 |
1.6
22 Dec 2017 01:30:27
|
jwb |
[new port] biology/canu: Single molecule sequence assembler
Approved by: jrm (mentor) or wen (mentor)
Differential Revision: https://reviews.freebsd.org/D13574 |
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