| Port details |
- subread High-performance read alignment, quantification and mutation discovery
- 2.0.2 biology
 =0      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: 2021-04-07 08:09:01
- Commit Hash: cf118cc
- License: GPLv3
- 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.
WWW: http://bioinf.wehi.edu.au/subread-package/
- SVNWeb : git : Homepage
- 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
- PKGNAME: subread
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1617112862
SHA256 (subread-2.0.2-source.tar.gz) = 0b64bd51f39f8d322c4594697fa5f0f64fbe60283113eadadff9f4268f897079
SIZE (subread-2.0.2-source.tar.gz) = 23295764
- 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>=4.3 : 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: 5
| Commit History - (may be incomplete: see SVNWeb link above for full details) |
| Date | By | Description |
|---|
07 Apr 2021 08:09:01
  2.0.2
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
06 Apr 2021 14:31:07
2.0.2
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
30 Mar 2021 15:30:27
  2.0.2
|
jwb |
biology/subread: Update to 2.0.2
Minor bug fixes and enhancements
Reported by: portscout |
18 Sep 2020 00:57:36
2.0.1
|
jwb |
biology/subread: Add -fcommon for clang 11
Reported by: pkg-fallout |
05 Jun 2020 01:55:49
2.0.1
|
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: 5
|
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