| Port details on branch 2022Q2 |
- cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
- 2.2.1.89_8 biology
 =0      2.2.1.89_8Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- 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.
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- 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:
- 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
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>=4.3 : devel/gmake
- python3.9 : lang/python39
- autoconf>=2.71 : devel/autoconf
- automake>=1.16.5 : devel/automake
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- python3.9 : lang/python39
- 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:
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