| Port details |
- gffread GFF/GTF format conversions, filtering, FASTA extraction, etc
- 0.12.9 biology
 =0      0.12.7Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-11-10 20:51:06
- Last Update: 2026-04-13 13:20:48
- Commit Hash: 945218c
- License: MIT
- WWW:
- https://ccb.jhu.edu/software/stringtie/gff.shtml
- Description:
- GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more. The program gffread can be used to validate,
filter, convert and perform various other operations on GFF files.
Because the program shares the same GFF parser code with Cufflinks,
Stringtie, and gffcompare, it could be used to verify that a GFF file
from a certain annotation source is correctly "understood" by these
programs.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - USE_RC_SUBR (Service Scripts)
- no SUBR information found for this port
- Dependency lines:
-
- gffread>0:biology/gffread
- Conflicts:
- CONFLICTS_INSTALL:
- To install the port:
- cd /usr/ports/biology/gffread/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/gffread
- pkg install gffread
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: gffread
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1776080973
SHA256 (gpertea-gffread-v0.12.9_GH0.tar.gz) = 92eb4a52fdd14c5fd3684041ef2d040c44d7414d076467a326eea2efa087a085
SIZE (gpertea-gffread-v0.12.9_GH0.tar.gz) = 408710
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>=4.4.1 : devel/gmake
- This port is required by:
- for Run
-
- biology/biostar-tools
- biology/rna-seq
Configuration Options:- No options to configure
- Options name:
- biology_gffread
- USES:
- gmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 7
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.12.9
13 Apr 2026 13:20:48
 |
Jason W. Bacon (jwb) |
biology/gffread: Update to 0.12.9
Fix buffer overflow
Changes: https://github.com/gpertea/gffread/releases
Reported by: portscout |
0.12.7
17 Mar 2026 21:29:31
|
Tobias Kortkamp (tobik) |
*: Fix WWW with broken anchors-as-comments
Case 1: WWW=https://example.com#foo
Here #foo is not part of the value of WWW since # introduces a comment
whether it's part of a word or not (quoting the word+# makes no
difference either). # needs to be escaped:
WWW=https://example.com\#foo
Case 2: WWW=https://example.com #foo
This is probably fallout from when WWW was moved from pkg-descr to
Makefile.
The anchors still exist on the actual websites too or I removed them. |
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) |
0.12.7
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  ) |
0.12.7
07 Mar 2022 22:44:38
|
Rene Ladan (rene) |
biology/gffread: remove local poudriere files |
0.12.7
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 ) |
0.12.7
10 Nov 2021 20:49:10
|
Jason W. Bacon (jwb) |
biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc
GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more. |
Number of commits found: 7
|
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