biology/bowtie 1.3.1
Ultrafast, memory-efficient short read aligner
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- ART10
- Categories
- biology
- Package size
- 7060.6 KiB, 14851.0 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.
Install
As a binary package — by origin, or by package name:
pkg install biology/bowtie
pkg install bowtieFrom the ports tree:
cd /usr/ports/biology/bowtie/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= bowtie>0:biology/bowtiePackages
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 | 1.3.1 | 1.3.1 | - | - | - |
| FreeBSD:14:quarterly | 1.3.1 | 1.3.1 | n/a | - | - |
| FreeBSD:15:latest | 1.3.1 | 1.3.1 | n/a | - | - |
| FreeBSD:15:quarterly | 1.3.1 | 1.3.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.3.1 | 1.3.1 | 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.
All build dependencies 3
All run dependencies 8
No port depends on this one.
Configuration
Options name: biology_bowtie
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
- USES
- compiler:c++11-lib gmake perl5 python:run shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The bowtie 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 92
- bin/bowtie
- bin/bowtie-align-l
- bin/bowtie-align-s
- bin/bowtie-build
- bin/bowtie-build-l
- bin/bowtie-build-s
- bin/bowtie-inspect
- bin/bowtie-inspect-l
- bin/bowtie-inspect-s
- share/bowtie/genomes/.cvsignore
- share/bowtie/genomes/NC_008253.fna
- share/bowtie/indexes/e_coli.1.ebwt
- share/bowtie/indexes/e_coli.2.ebwt
- share/bowtie/indexes/e_coli.3.ebwt
- share/bowtie/indexes/e_coli.4.ebwt
- share/bowtie/indexes/e_coli.README
- share/bowtie/indexes/e_coli.rev.1.ebwt
- share/bowtie/indexes/e_coli.rev.2.ebwt
- share/bowtie/reads/e_coli_1000.fa
- share/bowtie/reads/e_coli_1000.fq
- share/bowtie/reads/e_coli_1000.raw
- share/bowtie/reads/e_coli_10000snp.csfasta
- share/bowtie/reads/e_coli_10000snp.fa
- share/bowtie/reads/e_coli_10000snp.fq
- share/bowtie/reads/e_coli_1000_1.fa
- share/bowtie/reads/e_coli_1000_1.fq
- share/bowtie/reads/e_coli_1000_2.fa
- share/bowtie/reads/e_coli_1000_2.fq
- share/bowtie/reads/e_coli_1000_interleaved.fq
- share/bowtie/scripts/best_verify.pl
- share/bowtie/scripts/bowtie-hbb.sh
- share/bowtie/scripts/bs_mapability.pl
- share/bowtie/scripts/build_test.sh
- share/bowtie/scripts/colorize_fasta.pl
- share/bowtie/scripts/colorize_fastq.pl
- share/bowtie/scripts/convert_quals.pl
- share/bowtie/scripts/fastq_to_tabbed.pl
- share/bowtie/scripts/gen_2b_occ_lookup.pl
- share/bowtie/scripts/gen_dnamasks2colormask.pl
- share/bowtie/scripts/gen_occ_lookup.pl
- share/bowtie/scripts/gen_solqual_lookup.pl
- share/bowtie/scripts/infer_fraglen.pl
- share/bowtie/scripts/make_a_thaliana_tair.sh
- share/bowtie/scripts/make_b_taurus_UMD3.sh
- share/bowtie/scripts/make_c_elegans.sh
- share/bowtie/scripts/make_canFam2.sh
- share/bowtie/scripts/make_d_melanogaster.sh
- share/bowtie/scripts/make_e_coli.sh
- share/bowtie/scripts/make_galGal3.sh
- share/bowtie/scripts/make_h_sapiens_ncbi36.sh
- share/bowtie/scripts/make_h_sapiens_ncbi37.sh
- share/bowtie/scripts/make_hg18.sh
- share/bowtie/scripts/make_hg19.sh
- share/bowtie/scripts/make_m_musculus_ncbi37.sh
- share/bowtie/scripts/make_mm8.sh
- share/bowtie/scripts/make_mm9.sh
- share/bowtie/scripts/make_rn4.sh
- share/bowtie/scripts/make_s_cerevisiae.sh
- share/bowtie/scripts/mapability.pl
- share/bowtie/scripts/pe_verify.pl
- share/bowtie/scripts/reconcile_alignments.pl
- share/bowtie/scripts/reconcile_alignments_pe.pl
- share/bowtie/scripts/run-hbb.sh
- share/doc/bowtie/README
- share/doc/bowtie/manual.html
- share/doc/bowtie/release.txt
- share/doc/bowtie/strip_markdown.pl
- share/doc/bowtie/style.css
- share/doc/bowtie/website/css/style.css
- share/doc/bowtie/website/foot.ssi
- share/doc/bowtie/website/images/bowtie_logo.png
- share/doc/bowtie/website/images/osi-certified.gif
- share/doc/bowtie/website/images/sflogo.png
- share/doc/bowtie/website/images/university.small.horizontal.white.png
- share/doc/bowtie/website/index.html
- share/doc/bowtie/website/index.shtml
- share/doc/bowtie/website/latest-version.txt
- share/doc/bowtie/website/manual.html
- share/doc/bowtie/website/manual.shtml
- share/doc/bowtie/website/manual.ssi
- share/doc/bowtie/website/md5s.shtml
- share/doc/bowtie/website/md5s.ssi
- share/doc/bowtie/website/news.shtml
- share/doc/bowtie/website/old_news.ssi
- share/doc/bowtie/website/other_tools.shtml
- share/doc/bowtie/website/other_tools.ssi
- share/doc/bowtie/website/push.sh
- share/doc/bowtie/website/recent_news.ssi
- share/doc/bowtie/website/rhsidebar.ssi
- share/doc/bowtie/website/top.ssi
- share/doc/bowtie/website/tutorial.html
- share/doc/bowtie/website/tutorial.shtml
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| BenLangmead-bowtie-v1.3.1_GH0.tar.gz | 7.672741e+06 | 147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573 |