| Port details |
- cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
- 2.2.1.89_11 biology
 =2      2.2.1.89_10Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-05-25 22:28:39
- Last Update: 2025-02-14 03:17:22
- Commit Hash: fa53920
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSL
- WWW:
- https://cole-trapnell-lab.github.io/cufflinks/
- Description:
- Cufflinks assembles transcripts, estimates their abundances, and tests for
differential expression and regulation in RNA-Seq samples. It accepts aligned
RNA-Seq reads and assembles the alignments into a parsimonious set of
transcripts. Cufflinks then estimates the relative abundances of these
transcripts based on how many reads support each one, taking into account biases
in library preparation protocols.
Cufflinks was originally developed as part of a collaborative effort between the
Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC
Berkeley, Steven Salzberg's computational genomics group at the Institute of
Genetic Medicine at Johns Hopkins University, and Barbara Wold's lab at Caltech.
The project is now maintained by Cole Trapnell's lab at the University of
Washington.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- cufflinks>0:biology/cufflinks
- Conflicts:
- CONFLICTS_INSTALL:
- To install the port:
- cd /usr/ports/biology/cufflinks/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/cufflinks
- pkg install cufflinks
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: cufflinks
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1585636520
SHA256 (cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz) = 3947a7266b4f58a92b3944b8e205c8875a7c0ce9ea19b394ea82ff77b91999be
SIZE (cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz) = 8807044
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:
-
- eigen3.pc : math/eigen3
- gmake>=4.4.1 : devel/gmake
- python3.11 : lang/python311
- autoconf>=2.72 : devel/autoconf
- automake>=1.17 : devel/automake
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- python3.11 : lang/python311
- Library dependencies:
-
- libboost_system.so : devel/boost-libs
- libhts.so : biology/htslib
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_cufflinks
- USES:
- autoreconf compiler:c++11-lang eigen:3 gmake python shebangfix
- 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 |
|---|
2.2.1.89_11
14 Feb 2025 03:17:22
 |
Dima Panov (fluffy) |
devel/boost: bump consumers after Boost-1.87 update
Sponsored by: Future Crew, LLC |
2.2.1.89_10
20 Nov 2024 10:05:25
|
Dima Panov (fluffy) |
devel/boost: bump consu,ers after update Boost to 1.86 release
Sponsored by: Future Crew, LLC |
2.2.1.89_9
03 Oct 2024 10:25:14
|
Dima Panov (fluffy) |
*/*: bump consumers after devel/boost* update
With hat: office
Sponsored by: Future Crew, LLC |
2.2.1.89_8
13 Feb 2024 14:44:22
|
Dima Panov (fluffy) |
devel/boost: bump consumers after library update |
2.2.1.89_7
27 Sep 2023 14:36:30
|
Dima Panov (fluffy) |
devel/boost*: bump all consumers after 1.83.0 |
2.2.1.89_6
27 Apr 2023 18:25:55
|
Dima Panov (fluffy) |
*/*: bump all direct Boost cunsumers |
2.2.1.89_5
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
2.2.1.89_4
16 Jan 2023 19:32:07
|
Dima Panov (fluffy) |
*/*: bump libboost*.so libraries consumert after Boost upgrade |
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) |
2.2.1.89_3
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  ) |
2.2.1.89_3
12 Aug 2022 14:46:53
|
Dima Panov (fluffy) |
*/*: bump all consumers after recent boost upgrade |
2.2.1.89_2
28 Jul 2022 03:43:06
|
Yuri Victorovich (yuri) |
biology/cufflinks: Unbreak |
2.2.1.89_2
22 May 2022 20:17:09
|
Dima Panov (fluffy) |
biology/cufflinks: mark as BROKEN after recent boost upgrade
PR: 246106 |
2.2.1.89_2
10 Jan 2022 15:15:39
|
Stefan Eßer (se) |
Fix CONFLICTS entries of multiple ports
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.
This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.
Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port (Only the first 15 lines of the commit message are shown above ) |
2.2.1.89_2
12 Dec 2021 18:46:22
|
Tijl Coosemans (tijl) |
devel/automake: update to 1.16.5 |
2.2.1.89_2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.2.1.89_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.2.1.89_2
12 Dec 2020 17:04:37
 |
thierry |
- Upgrade math/eigen3 to 3.3.8;
- Add some dependencies which might be detected by Find_Package but not
registered;
- Bump PORTREVISION of consumers.
PR: 250833
Submitted by: /me
Approved by: tcberner@ (KDE / maintainer) + exp-run |
2.2.1.89_1
28 Aug 2020 18:24:04
|
tcberner |
biology/cufflinks: fix build on recent current |
2.2.1.89_1
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 |
2.2.1.89
08 Jul 2020 10:37:07
|
pkubaj |
biology/cufflinks: fix build on GCC architectures
Using Boost requires modern compiler.
MFH: 2020Q3 (fix build blanket) |
2.2.1.89
31 Mar 2020 06:42:23
|
yuri |
biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89
Add the pull request that fixes the boost::thread build failures. |
2.2.1.83_2
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 |
2.2.1.83_1
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 |
2.2.1.83
29 May 2019 07:02:28
|
yuri |
biology/cufflinks: Fix build on i386 by removing the hard-coded -m64
Reported by: fallout |
2.2.1.83
25 May 2019 22:28:12
|
yuri |
New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their
abundance, etc |
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