biology/stringtie 2.1.1
Transcript assembly and quantification for RNA-seq
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- MIT
- Categories
- biology
- Package size
- 273.2 KiB, 660.5 KiB installed
Description
StringTie is a fast and highly efficient assembler of RNA-seq alignments into potential transcripts. The input can be the alignments of raw reads as usual; it also accepts longer assembled sequences. The output can be processed by downstream software including Ballgown, Cuffdiff, etc.
Citation: Pertea et al. (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122
Install
As a binary package — by origin, or by package name:
pkg install biology/stringtie
pkg install stringtieFrom the ports tree:
cd /usr/ports/biology/stringtie/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= stringtie>0:biology/stringtiePackages
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 | 2.1.1 | 2.1.1 | 2.1.1 |
| FreeBSD:14:quarterly | 2.1.1 | 2.1.1 | n/a | 2.1.1 | 2.1.1 |
| FreeBSD:15:latest | 2.1.1 | 2.1.1 | n/a | 2.1.1 | 2.1.1 |
| 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.
Test 2
bash: shells/bashcurl: ftp/curl
The full lists below include those, and their dependencies in turn.
All build dependencies 3
Configuration
No options to configure.
- USES
- compiler:c++11-lang gmake
- Service scripts
- none
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| stringtie-2.1.1.tar.gz | 1.969917e+06 | 7ea152b791856b1bd5dd2d475b06fae05398ee7e03f2f9844418010376edcca2 |
Master sites 1
- http://ccb.jhu.edu/software/stringtie/dl/
Commit history 0
No commits in the history this site was built from.