BSD Portsbiology/hisat2 2.2.3 FreeBSD
Alignment program for mapping next-generation sequencing reads
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv3
- Categories
- biology, perl5, python
- Package size
- 1033.4 KiB, 4334.9 KiB installed
Description
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
In the other systems
The newest version among them is 2.2.3, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/hisat2 | 2.2.3 newest | none known | - | [email protected] | 2026-10-08 |
| NetBSD | biology/hisat2 | 2.2.1nb4 | none known | - | [email protected] | 2026-08-04 |
| DragonFly | biology/hisat2 | 2.2.1_2 | none known | - | [email protected] | - |
| HardenedBSD | biology/hisat2 | 2.2.3 newest | no data | - | [email protected] | - |
| GhostBSD | biology/hisat2 | 2.2.3 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install hisat2From the ports tree:
cd /usr/ports/biology/hisat2/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= hisat2>0:biology/hisat2Packages
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 | 2.2.3 | 2.2.3 | - | - | - |
| FreeBSD:14:quarterly | 2.2.3 | 2.2.3 | n/a | - | - |
| FreeBSD:15:latest | 2.2.3 | 2.2.3 | n/a | - | - |
| FreeBSD:15:quarterly | 2.2.3 | 2.2.3 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.2.3 | 2.2.3 | 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.
Build 1
simde>0: devel/simde
The full lists below include those, and their dependencies in turn.
Build dependencies 10
Run dependencies 8
Required by 2
Configuration
No options to configure.
- USES
- gmake localbase perl5 python shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The hisat2 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 66
- bin/hisat2
- bin/hisat2-align-l
- bin/hisat2-align-s
- bin/hisat2-build
- bin/hisat2-build-l
- bin/hisat2-build-s
- bin/hisat2-inspect
- bin/hisat2-inspect-l
- bin/hisat2-inspect-s
- bin/hisat2-repeat
- libexec/hisat2/convert_quals.pl
- libexec/hisat2/extract_exons.py
- libexec/hisat2/extract_splice_sites.py
- libexec/hisat2/gen_2b_occ_lookup.pl
- libexec/hisat2/gen_occ_lookup.pl
- libexec/hisat2/gen_solqual_lookup.pl
- libexec/hisat2/hisat2_extract_exons.py
- libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
- libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
- libexec/hisat2/hisat2_extract_splice_sites.py
- libexec/hisat2/hisat2_read_statistics.py
- libexec/hisat2/hisat2_simulate_reads.py
- libexec/hisat2/infer_fraglen.pl
- libexec/hisat2/make_a_thaliana_tair.sh
- libexec/hisat2/make_b_taurus_UMD3.sh
- libexec/hisat2/make_bdgp6.sh
- libexec/hisat2/make_bdgp6_tran.sh
- libexec/hisat2/make_canFam2.sh
- libexec/hisat2/make_ce10.sh
- libexec/hisat2/make_dm6.sh
- libexec/hisat2/make_e_coli.sh
- libexec/hisat2/make_grch37.sh
- libexec/hisat2/make_grch37_snp.sh
- libexec/hisat2/make_grch37_snp_tran.sh
- libexec/hisat2/make_grch37_snp_tran_ercc.sh
- libexec/hisat2/make_grch37_tran.sh
- libexec/hisat2/make_grch38.sh
- libexec/hisat2/make_grch38_rep.sh
- libexec/hisat2/make_grch38_snp.sh
- libexec/hisat2/make_grch38_snp_rep.sh
- libexec/hisat2/make_grch38_snp_tran.sh
- libexec/hisat2/make_grch38_snp_tran_ercc.sh
- libexec/hisat2/make_grch38_tran.sh
- libexec/hisat2/make_grcm38.sh
- libexec/hisat2/make_grcm38_snp.sh
- libexec/hisat2/make_grcm38_snp_tran.sh
- libexec/hisat2/make_grcm38_tran.sh
- libexec/hisat2/make_hg19.sh
- libexec/hisat2/make_hg38.sh
- libexec/hisat2/make_hg38_allsnp.sh
- libexec/hisat2/make_hg38_snp.sh
- libexec/hisat2/make_hg38_snp_tran.sh
- libexec/hisat2/make_mm10.sh
- libexec/hisat2/make_mm9.sh
- libexec/hisat2/make_r64.sh
- libexec/hisat2/make_r64_tran.sh
- libexec/hisat2/make_rn4.sh
- libexec/hisat2/make_rn6.sh
- libexec/hisat2/make_rnor6.sh
- libexec/hisat2/make_rnor6_tran.sh
- libexec/hisat2/make_sc3.sh
- libexec/hisat2/make_wbcel235.sh
- libexec/hisat2/make_wbcel235_tran.sh
- libexec/hisat2/make_zm3_snp_tran_ercc.sh
- libexec/hisat2/sa.py
- libexec/hisat2/validate_repeat.py
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| DaehwanKimLab-hisat2-v2.2.3_GH0.tar.gz | 7.059086e+06 | b53107422e5b44ebea4b20b1a77bb9e240d6b92d654fcd7e6a6ab5d1aae86c45 |