biology/chip-seq 0.3.1
Metaport for ChIP-Seq analysis
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
10768ab4fb- License
- BSD2CLAUSE
- Categories
- biology, python
Description
Metaport to install tools for typical ChIP-Seq analysis, including QC, adapter trimming, alignment, and differential analysis.
Install
As a binary package — by origin, or by package name:
pkg install biology/chip-seq
pkg install chip-seqFrom the ports tree:
cd /usr/ports/biology/chip-seq/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= chip-seq>0:biology/chip-seqPackages
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 | - | 0.3.1 | n/a | - | - |
| FreeBSD:15:quarterly | - | 0.3.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 0.3.1 | 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 14
sra-tools>0: biology/sra-toolsfastq-trim>0: biology/fastq-trimfastqc>0: biology/fastqc${PYTHON_PKGNAMEPREFIX}multiqc>0: biology/py-multiqcbiolibc-tools>0: biology/biolibc-toolsbwa>0: biology/bwabowtie2>0: biology/bowtie2samtools>0: biology/samtools${PYTHON_PKGNAMEPREFIX}MACS3>0: biology/py-macs3fasda>0: biology/fasdafasda-utils>0: biology/fasda-utilspeak-classifier>0: biology/peak-classifierwebbrowser>0: www/webbrowsercurl>0: ftp/curl
The full lists below include those, and their dependencies in turn.
All build dependencies 7
All run dependencies 409
- accessibility/at-spi2-core
- accessibility/speech-dispatcher
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/lzo2
- archivers/minizip
- archivers/py-brotli
- archivers/py-zopfli
- archivers/snappy
- 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/bedtools
- biology/biolibc
- biology/biolibc-tools
- biology/bowtie2
- biology/bwa
- biology/fasda
- biology/fasda-utils
- biology/fastq-trim
- biology/fastqc
- biology/htslib
- biology/peak-classifier
- biology/py-macs3
- biology/py-multiqc
- biology/samtools
- biology/sra-tools
- biology/stringtie
- converters/fribidi
- converters/libiconv
- databases/arrow
- databases/gdbm
- databases/postgresql18-client
- databases/py-pyarrow
- databases/py-sqlite3
- databases/sfcgal
- databases/spatialite
- databases/sqlite3
- devel/abseil
- devel/aws-c-common
- devel/aws-c-compression
- devel/aws-c-event-stream
- devel/aws-c-http
- devel/aws-c-io
- devel/aws-c-mqtt
- devel/aws-c-s3
- devel/aws-c-sdkutils
- devel/aws-checksums
- devel/aws-crt-cpp
- devel/aws-sdk-cpp
- devel/benchmark
- devel/binutils
- devel/boost-libs
- devel/dbus
- devel/dbus-glib
- devel/dconf
- devel/desktop-file-utils
- devel/dotconf
- devel/gettext-runtime
- devel/gflags
- devel/glib20
- devel/gobject-introspection
- devel/googletest
- devel/grpc
- devel/gsettings-desktop-schemas
- devel/icu
- devel/json-c
- devel/json-glib
- devel/jsoncpp
- devel/libdaemon
- devel/libdatrie
- devel/libedit
- devel/libepoll-shim
- devel/libev
- devel/libevdev
- devel/libevent
- devel/libffi
- devel/libgudev
- devel/libgusb
- devel/libinotify
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.