BSD Portsbiology/subread 2.1.1 FreeBSD
High-performance read alignment, quantification and mutation discovery
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv3
- Categories
- biology
- Package size
- 759.9 KiB, 7803.4 KiB installed
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.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/subread | 2.1.1 |
| NetBSD | wip/subread | 2.1.0 |
| DragonFly | biology/subread | 2.1.0 |
| HardenedBSD | biology/subread | 2.1.1 |
| GhostBSD | biology/subread | 2.1.1 |
Install
Binary package:
pkg install subreadFrom the ports tree:
cd /usr/ports/biology/subread/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= subread>0:biology/subreadPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.1.1 | 2.1.1 | 2.0.2 | 2.1.0 | 2.1.1 |
| FreeBSD:14:quarterly | 2.1.1 | 2.1.1 | n/a | 2.1.0 | 2.1.1 |
| FreeBSD:15:latest | 2.1.1 | 2.1.1 | n/a | 2.1.0 | 2.1.0 |
| FreeBSD:15:quarterly | 2.1.1 | 2.1.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.1.1 | 2.1.1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 1
libsysinfo.so: devel/libsysinfo
The full lists below include those, and their dependencies in turn.
Build dependencies 4
Run dependencies 1
Required by 1
Configuration
No options to configure.
- USES
- gmake localbase:ldflags
- Service scripts
- none
Files
pkg-plist 16
- bin/detectionCall
- bin/exactSNP
- bin/featureCounts
- bin/flattenGTF
- bin/genRandomReads
- bin/propmapped
- bin/qualityScores
- bin/removeDup
- bin/repair
- bin/subindel
- bin/subjunc
- bin/sublong
- bin/subread-align
- bin/subread-buildindex
- bin/subread-fullscan
- bin/txUnique
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| subread-2.1.1-source.tar.gz | 2.6095717e+07 | 6392d7c66831cdd767e58251892a79a51b6fab8ed0ba9671ad5e85ff1ab01eaa |
Master sites 1
- SF/subread/subread-${PORTVERSION}