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Port details
gffread GFF/GTF format conversions, filtering, FASTA extraction, etc
0.12.7 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 0.12.7Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-11-10 20:51:06
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: MIT
WWW:
http://ccb.jhu.edu/software/stringtie/gff.shtml
Description:
GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/gffread
  2. /usr/local/share/licenses/gffread-0.12.7/catalog.mk
  3. /usr/local/share/licenses/gffread-0.12.7/LICENSE
  4. /usr/local/share/licenses/gffread-0.12.7/MIT
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Dependency lines:
  • gffread>0:biology/gffread
Conflicts:
CONFLICTS_INSTALL:
  • cufflinks
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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 = 1636511584 SHA256 (gpertea-gffread-v0.12.7_GH0.tar.gz) = 6f3417090b3beb74f435bf5d462c87475b3c704a8a0d71821f6c1321c47dbbbe SIZE (gpertea-gffread-v0.12.7_GH0.tar.gz) = 403734

Expand this list (2 items)

Collapse this list.

SHA256 (gpertea-gclib-v0.12.7_GH0.tar.gz) = 9c74db64c4ee1fb93a6c02fa227258baafc337303f26ce3ba0cf37dfc1ba687f SIZE (gpertea-gclib-v0.12.7_GH0.tar.gz) = 259314

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Packages (timestamps in pop-ups are UTC):
gffread
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.12.70.12.7-0.12.70.12.7---
FreeBSD:13:quarterly0.12.70.12.70.12.70.12.70.12.70.12.70.12.70.12.7
FreeBSD:14:latest0.12.70.12.70.12.70.12.70.12.70.12.7-0.12.7
FreeBSD:14:quarterly0.12.70.12.7-0.12.70.12.70.12.70.12.70.12.7
FreeBSD:15:latest0.12.70.12.7n/a0.12.7n/a0.12.70.12.70.12.7
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. gmake>=4.3 : devel/gmake
This port is required by:
for Run
  1. biology/biostar-tools
  2. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/gpertea/gffread/tar.gz/v0.12.7?dummy=/
Collapse this list.

Number of commits found: 5

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
0.12.7
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)
0.12.7
07 Mar 2022 22:44:38
commit hash: 4e051b961c7e0a940fd8e183113d85223b5b3f72commit hash: 4e051b961c7e0a940fd8e183113d85223b5b3f72commit hash: 4e051b961c7e0a940fd8e183113d85223b5b3f72commit hash: 4e051b961c7e0a940fd8e183113d85223b5b3f72 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
biology/gffread: remove local poudriere files
0.12.7
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)
0.12.7
10 Nov 2021 20:49:10
commit hash: 8d2198bb6d6b84739448087c8284079281149086commit hash: 8d2198bb6d6b84739448087c8284079281149086commit hash: 8d2198bb6d6b84739448087c8284079281149086commit hash: 8d2198bb6d6b84739448087c8284079281149086 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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: 5