BSD Portsbiology/biostar-tools 2.1 FreeBSD
Meta-port for Biostar Handbook tools
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
10768ab4fb- License
- BSD2CLAUSE
- Categories
- biology, python
Description
Biostar-Tools is a metaport for installing all the tools necessary to work through the Biostar Handbook.
The handbook instructs the reader to install these tools mostly via bioconda, which then requires the user to activate the bioconda environment each time they want to use the tools. You can also install conda packages on FreeBSD if you wish. For details, see
/usr/ports/sysutils/linux-miniconda-installer/pkg-descr
Biostar-tools installs all of the tools except emboss to the default PATH (normally /usr/local/bin) so they just work without any special environment. Emboss commands are installed to /usr/local/emboss/bin due to conflicts with other packages. Run "biostar-shell" to add the emboss commands to your PATH, and simply exit the shell to return your PATH to normal.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/biostar-tools | 2.1 |
| NetBSD | wip/biostar-tools | 1.10.1 |
Install
Binary package:
pkg install biostar-toolsFrom the ports tree:
cd /usr/ports/biology/biostar-tools/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= biostar-tools>0:biology/biostar-toolsPackages
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 | - | - | - | - | - |
| FreeBSD:14:quarterly | - | - | n/a | - | - |
| FreeBSD:15:latest | - | - | n/a | - | - |
| FreeBSD:15:quarterly | - | - | n/a | n/a | n/a |
| FreeBSD:16:latest | - | - | 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 53
wget>0: ftp/wgetcurl>0: ftp/curlnano>0: editors/nanoparallel>0: sysutils/parallelseqkit>0: biology/seqkitcsvtk>0: science/csvtk${PYTHON_PKGNAMEPREFIX}csvkit>0: textproc/py-csvkitmiller>0: textproc/millerncbi-entrez-direct>0: biology/ncbi-entrez-directreadseq>0: biology/readseqpicard-tools>0: biology/picard-toolsbbmap>0: biology/bbmapminimap2>0: biology/minimap2bwa>0: biology/bwabowtie2>0: biology/bowtie2samtools>0: biology/samtoolsemboss>0: biology/embossbedtools>0: biology/bedtoolsbamtools>0: biology/bamtools${PYTHON_PKGNAMEPREFIX}cutadapt>0: biology/py-cutadaptseqtk>0: biology/seqtkdatamash>0: textproc/datamashbcftools>0: biology/bcftoolssubread>0: biology/subreadhisat2>0: biology/hisat2trimmomatic>0: biology/trimmomaticfastqc>0: biology/fastqcpicard-tools>0: biology/picard-toolsncbi-blast+>0: biology/ncbi-blast+cd-hit>0: biology/cd-hit${PYTHON_PKGNAMEPREFIX}biopython>0: biology/py-biopython${PYTHON_PKGNAMEPREFIX}pysam>0: biology/py-pysamfreebayes>0: biology/freebayesp5-Net-SSLeay>0: security/p5-Net-SSLeaybioawk>0: biology/bioawkvt>0: biology/vt${PYTHON_PKGNAMEPREFIX}crossmap>0: biology/py-crossmap${PYTHON_PKGNAMEPREFIX}goatools>0: biology/py-goatoolserminej>0: biology/erminej${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0: biology/py-ont-fast5-api${PYTHON_PKGNAMEPREFIX}multiqc>0: biology/py-multiqcflash>0: biology/flashbfc: biology/bfcJellyfish>0: biology/jellyfishmafft>0: biology/mafftclustal-omega>0: biology/clustal-omegasam2pairwise>0: biology/sam2pairwisekallisto>0: biology/kallistobamutil>0: biology/bamutil${PYTHON_PKGNAMEPREFIX}deepTools>0: biology/py-deeptoolsigv>0: biology/igvgffread>0: biology/gffreaducsc-userapps>0: biology/ucsc-userapps
The full lists below include those, and their dependencies in turn.
Build dependencies 7
Run dependencies 535
- accessibility/at-spi2-core
- accessibility/speech-dispatcher
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/lzo2
- archivers/minizip
- archivers/pbzip2
- archivers/pigz
- archivers/py-brotli
- archivers/py-xopen
- archivers/py-zopfli
- archivers/py-zstandard
- archivers/snappy
- archivers/vbz-compression
- archivers/zopfli
- archivers/zstd
- audio/alsa-lib
- audio/alsa-plugins
- audio/ebur128
- audio/espeak-ng
- audio/flac
- audio/jack
- audio/lame
- audio/libogg
- audio/libsamplerate
- audio/libsndfile
- audio/libsoxr
- audio/libvorbis
- audio/mpg123
- audio/opus
- audio/pcaudiolib
- audio/pulseaudio
- audio/sndio
- audio/speex
- audio/speexdsp
- audio/webrtc-audio-processing
- biology/bamtools
- biology/bamutil
- biology/bbmap
- biology/bcftools
- biology/bedtools
- biology/bfc
- biology/bioawk
- biology/bowtie2
- biology/bwa
- biology/cd-hit
- biology/clustal-omega
- biology/emboss
- biology/erminej
- biology/fastqc
- biology/flash
- biology/freebayes
- biology/gffread
- biology/hisat2
- biology/htslib
- biology/igv
- biology/jellyfish
- biology/kallisto
- biology/mafft
- biology/minimap2
- biology/ncbi-blast+
- biology/ncbi-entrez-direct
- biology/picard-tools
- biology/py-biopython
- biology/py-bx-python
- biology/py-crossmap
- biology/py-cutadapt
- biology/py-deeptools
- biology/py-deeptoolsintervals
- biology/py-dnaio
- biology/py-goatools
- biology/py-multiqc
- biology/py-ont-fast5-api
- biology/py-py2bit
- biology/py-pybigwig
- biology/py-pysam
- biology/readseq
- biology/sam2pairwise
- biology/samtools
- biology/seqkit
- biology/seqtk
- biology/subread
- biology/trimmomatic
- biology/ucsc-userapps
- biology/vt
- converters/fribidi
- converters/libiconv
- converters/p5-Encode-Locale
- converters/p5-JSON
- converters/p5-MIME-Base32
- converters/p5-MIME-Base64
- converters/py-text-unidecode
- databases/arrow
- databases/gdbm
- databases/lmdb0
- databases/mysql84-client
- databases/openldap26-client
- databases/postgresql18-client
- databases/py-agate-sql
The first 100 are listed.
No port depends on this one.
Configuration
No options to configure.
- USES
- metaport python
- Service scripts
- none
Files
No file lists for this port.