| Port details |
- subread High-performance read alignment, quantification and mutation discovery
- 2.1.0 biology
 =2      2.0.2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2020-06-05 01:55:58
- Last Update: 2025-03-27 22:05:26
- Commit Hash: 888c0b0
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://subread.sourceforge.net/
- Description:
- The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:
Subread: a general-purpose read aligner which can align both genomic
DNA-seq and RNA-seq reads. It can also be used to discover genomic
mutations including short indels and structural variants.
Subjunc: a read aligner developed for aligning RNA-seq reads and for the
detection of exon-exon junctions. Gene fusion events can be detected as
well.
featureCounts: a software program developed for counting reads to genomic
features such as genes, exons, promoters and genomic bins.
Sublong: a long-read aligner that is designed based on seed-and-vote.
exactSNP: a SNP caller that discovers SNPs by testing signals against local
background noises.
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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:
-
- subread>0:biology/subread
- To install the port:
- cd /usr/ports/biology/subread/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/subread
- pkg install subread
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: subread
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1743112595
SHA256 (subread-2.1.0-source.tar.gz) = fdf8a84cf145edab4984070e71595612c97ad3741afdb8d25f93dae7c8703433
SIZE (subread-2.1.0-source.tar.gz) = 26090041
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
- Library dependencies:
-
- libsysinfo.so : devel/libsysinfo
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_subread
- USES:
- gmake localbase:ldflags
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 9
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.1.0
27 Mar 2025 22:05:26
 |
Jason W. Bacon (jwb) |
biology/subread: Update to 2.1.0
Improved identification and reporting of junctions in featureCounts
Changes: https://subread.sourceforge.net/ |
2.0.8
19 Jan 2025 12:46:51
|
Jason W. Bacon (jwb) |
biology/subread: Update to 2.0.8
A few fixes and updates since 2.0.2
Changes: https://subread.sourceforge.net/
PR: 283261
Reported by: alster@vinterdalen.se |
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) |
2.0.2
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  ) |
2.0.2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.0.2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.0.2
30 Mar 2021 15:30:27
 |
jwb |
biology/subread: Update to 2.0.2
Minor bug fixes and enhancements
Reported by: portscout |
2.0.1
18 Sep 2020 00:57:36
|
jwb |
biology/subread: Add -fcommon for clang 11
Reported by: pkg-fallout |
2.0.1
05 Jun 2020 01:55:49
|
jwb |
biology/subread: Read alignment, quantification and mutation discovery
The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:
Subread: a general-purpose read aligner
Subjunc: a read aligner developed for aligning RNA-seq reads
featureCounts: a software program developed for counting reads to genomic
features such as genes, exons, promoters and genomic bins.
Sublong: a long-read aligner that is designed based on seed-and-vote.
exactSNP: discovers SNPs by testing signals against local background noise. |
Number of commits found: 9
|
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