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Port details
cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
2.2.1.89_8 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 View this port on Repology. pkg-fallout 2.2.1.89_7Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-25 22:28:39
Last Update: 2024-02-13 14:44:22
Commit Hash: db61653
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (12 items)
Collapse this list.
  1. bin/compress_gtf
  2. bin/cuffcompare
  3. bin/cuffdiff
  4. bin/cufflinks
  5. bin/cuffmerge
  6. bin/cuffnorm
  7. bin/cuffquant
  8. bin/gffread
  9. bin/gtf_to_sam
  10. /usr/local/share/licenses/cufflinks-2.2.1.89_8/catalog.mk
  11. /usr/local/share/licenses/cufflinks-2.2.1.89_8/LICENSE
  12. /usr/local/share/licenses/cufflinks-2.2.1.89_8/BSL
Collapse this list.
Dependency lines:
  • cufflinks>0:biology/cufflinks
Conflicts:
CONFLICTS_INSTALL:
  • gffread
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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

Expand this list (2 items)

Collapse this list.

SHA256 (ea4671149f3054c773d99cea521db75bf7b0658f.patch) = d64446bab1b683dbdb51b33992694bbbc6511aa4eacd2b95812da75e090dff47 SIZE (ea4671149f3054c773d99cea521db75bf7b0658f.patch) = 3779

Collapse this list.


Packages (timestamps in pop-ups are UTC):
cufflinks
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.2.1.89_82.2.1.89_8-2.2.1.89_82.2.1.89_8---
FreeBSD:13:quarterly2.2.1.89_72.2.1.89_7-2.2.1.89_72.2.1.89_7-2.2.1.89_72.2.1.89_7
FreeBSD:14:latest2.2.1.89_82.2.1.89_8-2.2.1.89_82.2.1.89_8---
FreeBSD:14:quarterly2.2.1.89_72.2.1.89_7-2.2.1.89_72.2.1.89_7-2.2.1.89_72.2.1.89_7
FreeBSD:15:latest2.2.1.89_82.2.1.89_8n/a2.2.1.89_7n/a-2.2.1.89_72.2.1.89_8
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. eigen3.pc : math/eigen3
  2. gmake>=4.3 : devel/gmake
  3. python3.9 : lang/python39
  4. autoconf>=2.71 : devel/autoconf
  5. automake>=1.16.5 : devel/automake
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
Library dependencies:
  1. libboost_system.so : devel/boost-libs
  2. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/cole-trapnell-lab/cufflinks/tar.gz/v2.2.1-89-gdc3b0cb?dummy=/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.2.1.89_8
13 Feb 2024 14:44:22
commit hash: db616534ff99d6268997e2f30858891e20641a1ecommit hash: db616534ff99d6268997e2f30858891e20641a1ecommit hash: db616534ff99d6268997e2f30858891e20641a1ecommit hash: db616534ff99d6268997e2f30858891e20641a1e files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost: bump consumers after library update
2.2.1.89_7
27 Sep 2023 14:36:30
commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost*: bump all consumers after 1.83.0
2.2.1.89_6
27 Apr 2023 18:25:55
commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all direct Boost cunsumers
2.2.1.89_5
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2.2.1.89_4
16 Jan 2023 19:32:07
commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash: e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash: e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*:	bump libboost*.so libraries consumert after Boost upgrade
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
2.2.1.89_3
12 Aug 2022 14:46:53
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
2.2.1.89_2
28 Jul 2022 03:43:06
commit hash: 8fd55d46d939263df2c327093c6bb21d74a29c0dcommit hash: 8fd55d46d939263df2c327093c6bb21d74a29c0dcommit hash: 8fd55d46d939263df2c327093c6bb21d74a29c0dcommit hash: 8fd55d46d939263df2c327093c6bb21d74a29c0d files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/cufflinks: Unbreak
2.2.1.89_2
22 May 2022 20:17:09
commit hash: 1054b6f30ebfba3325a6d2cdb7bc1def670d3b31commit hash: 1054b6f30ebfba3325a6d2cdb7bc1def670d3b31commit hash: 1054b6f30ebfba3325a6d2cdb7bc1def670d3b31commit hash: 1054b6f30ebfba3325a6d2cdb7bc1def670d3b31 files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
biology/cufflinks: mark as BROKEN after recent boost upgrade

PR:	246106
2.2.1.89_2
10 Jan 2022 15:15:39
commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
2.2.1.89_2
12 Dec 2021 18:46:22
commit hash: 68b99b391349672d7f70e7ac89d430b8dbe32850commit hash: 68b99b391349672d7f70e7ac89d430b8dbe32850commit hash: 68b99b391349672d7f70e7ac89d430b8dbe32850commit hash: 68b99b391349672d7f70e7ac89d430b8dbe32850 files touched by this commit
Tijl Coosemans (tijl) search for other commits by this committer
devel/automake: update to 1.16.5
2.2.1.89_2
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.2.1.89_2
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.2.1.89_2
12 Dec 2020 17:04:37
Revision:557839Original commit files touched by this commit
thierry search for other commits by this committer
- 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
Revision:546790Original commit files touched by this commit
tcberner search for other commits by this committer
biology/cufflinks: fix build on recent current
2.2.1.89_1
03 Aug 2020 17:40:04
Revision:544090Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:541482Original commit files touched by this commit
pkubaj search for other commits by this committer
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
Revision:529953Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:519824Original commit files touched by this commit
jbeich search for other commits by this committer
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
Revision:509290Original commit files touched by this commit
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
2.2.1.83
29 May 2019 07:02:28
Revision:502929Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:502661Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their
abundance, etc

Number of commits found: 23