BSD Portsbiology/stacks 2.68 FreeBSD
Software pipeline for building loci from short-read sequences
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv2
- Categories
- biology, perl5, python
- Package size
- 1339.1 KiB, 6907.8 KiB installed
Description
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/stacks | 2.68 |
| NetBSD | biology/stacks | 2.68 |
| DragonFly | biology/stacks | 2.68 |
Install
Binary package:
pkg install stacksFrom the ports tree:
cd /usr/ports/biology/stacks/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= stacks>0:biology/stacksPackages
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 | 2.68 | 2.68 | 2.4_2 | 2.68 | 2.68 |
| FreeBSD:14:quarterly | 2.68 | 2.68 | n/a | 2.68 | 2.68 |
| FreeBSD:15:latest | 2.68 | 2.68 | n/a | 2.68 | 2.68 |
| FreeBSD:15:quarterly | 2.68 | 2.68 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.68 | 2.68 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
The Makefile names none itself; they come from USES and USE_*.
The full lists below include those, and their dependencies in turn.
Build dependencies 8
Run dependencies 7
No port depends on this one.
Configuration
No options to configure.
- USES
- gmake python shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The stacks port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing
Files
pkg-plist 20
- bin/clone_filter
- bin/cstacks
- bin/denovo_map.pl
- bin/gstacks
- bin/kmer_filter
- bin/phasedstacks
- bin/populations
- bin/process_radtags
- bin/process_shortreads
- bin/ref_map.pl
- bin/sstacks
- bin/stacks-count-reads-per-sample-per-locus
- bin/stacks-dist-extract
- bin/stacks-gdb
- bin/stacks-hist2d-loci-samples-coverage
- bin/stacks-integrate-alignments
- bin/stacks-private-alleles
- bin/stacks-samtools-tview
- bin/tsv2bam
- bin/ustacks
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| stacks-2.68.tar.gz | 1.5552836e+07 | 9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650 |
Master sites 1
- https://catchenlab.life.illinois.edu/stacks/source/