BSD Portsbiology/bowtie2 2.5.5 FreeBSD
Ultrafast, memory-efficient short read aligner
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv3+
- Categories
- biology, perl5, python
- Package size
- 9032.3 KiB, 24533.2 KiB installed
Description
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/bowtie2 | 2.5.5 |
| NetBSD | biology/bowtie2 | 2.5.4 |
| DragonFly | biology/bowtie2 | 2.5.4 |
| HardenedBSD | biology/bowtie2 | 2.5.5 |
| GhostBSD | biology/bowtie2 | 2.5.5 |
Install
Binary package:
pkg install bowtie2From the ports tree:
cd /usr/ports/biology/bowtie2/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= bowtie2>0:biology/bowtie2Packages
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 | 2.5.5 | 2.5.5 | - | - | - |
| FreeBSD:14:quarterly | 2.5.5 | 2.5.5 | n/a | - | - |
| FreeBSD:15:latest | 2.5.5 | 2.5.5 | n/a | - | - |
| FreeBSD:15:quarterly | 2.5.5 | 2.5.5 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.5.5 | 2.5.5 | 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.
Runtime 1
bash: shells/bash
The full lists below include those, and their dependencies in turn.
Build dependencies 8
Run dependencies 9
Required by 3
Configuration
Options name: biology_bowtie2
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
| EXAMPLES | off | Build and/or install examples |
- USES
- gmake localbase:ldflags perl5 python shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The bowtie2 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 69
- bin/bowtie2
- bin/bowtie2-align-l
- bin/bowtie2-align-l-v256
- bin/bowtie2-align-s
- bin/bowtie2-align-s-v256
- bin/bowtie2-build
- bin/bowtie2-build-l
- bin/bowtie2-build-s
- bin/bowtie2-inspect
- bin/bowtie2-inspect-l
- bin/bowtie2-inspect-s
- bin/bowtie2-test
- share/bowtie2/scripts/bowtie2-hbb.sh
- share/bowtie2/scripts/convert_quals.pl
- share/bowtie2/scripts/gen_2b_occ_lookup.pl
- share/bowtie2/scripts/gen_occ_lookup.pl
- share/bowtie2/scripts/gen_solqual_lookup.pl
- share/bowtie2/scripts/infer_fraglen.pl
- share/bowtie2/scripts/make_a_thaliana_tair.sh
- share/bowtie2/scripts/make_b_taurus_UMD3.sh
- share/bowtie2/scripts/make_c_elegans.sh
- share/bowtie2/scripts/make_canFam2.sh
- share/bowtie2/scripts/make_d_melanogaster.sh
- share/bowtie2/scripts/make_e_coli.sh
- share/bowtie2/scripts/make_h_sapiens_ncbi36.sh
- share/bowtie2/scripts/make_h_sapiens_ncbi37.sh
- share/bowtie2/scripts/make_hg18.sh
- share/bowtie2/scripts/make_hg19.sh
- share/bowtie2/scripts/make_m_musculus_ncbi37.sh
- share/bowtie2/scripts/make_mm10.sh
- share/bowtie2/scripts/make_mm9.sh
- share/bowtie2/scripts/make_rn4.sh
- share/bowtie2/scripts/make_s_cerevisiae.sh
- share/doc/bowtie2/README
- share/doc/bowtie2/images/bowtie_logo.png
- share/doc/bowtie2/images/osi-certified.gif
- share/doc/bowtie2/images/sflogo.png
- share/doc/bowtie2/images/university.small.horizontal.white.png
- share/doc/bowtie2/manual.html
- share/doc/bowtie2/release.txt
- share/doc/bowtie2/style.css
- share/doc/bowtie2/website/faq.shtml
- share/doc/bowtie2/website/faq.ssi
- share/doc/bowtie2/website/foot.ssi
- share/doc/bowtie2/website/index.html
- share/doc/bowtie2/website/index.shtml
- share/doc/bowtie2/website/manual.shtml
- share/doc/bowtie2/website/manual.ssi
- share/doc/bowtie2/website/news.shtml
- share/doc/bowtie2/website/old_news.ssi
- share/doc/bowtie2/website/other_tools.shtml
- share/doc/bowtie2/website/push.sh
- share/doc/bowtie2/website/push_images.sh
- share/doc/bowtie2/website/recent_news.ssi
- share/doc/bowtie2/website/rhsidebar.ssi
- share/doc/bowtie2/website/top.ssi
- share/examples/bowtie2/index/lambda_virus.1.bt2
- share/examples/bowtie2/index/lambda_virus.2.bt2
- share/examples/bowtie2/index/lambda_virus.3.bt2
- share/examples/bowtie2/index/lambda_virus.4.bt2
- share/examples/bowtie2/index/lambda_virus.rev.1.bt2
- share/examples/bowtie2/index/lambda_virus.rev.2.bt2
- share/examples/bowtie2/reads/combined_reads.bam
- share/examples/bowtie2/reads/conversion_utilities.sh
- share/examples/bowtie2/reads/longreads.fq
- share/examples/bowtie2/reads/reads_1.fq
- share/examples/bowtie2/reads/reads_2.fq
- share/examples/bowtie2/reads/simulate.pl
- share/examples/bowtie2/reference/lambda_virus.fa
distinfo 2
| File | Size | SHA256 |
|---|---|---|
| BenLangmead-bowtie2-v2.5.5_GH0.tar.gz | 1.0645909e+07 | e38d1833ec235ca27fa57589d32d897c9addf87085b7cb7bc978662954662da2 |
| simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz | 397743 | 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8 |