BSD Portsbiology/kallisto 0.52.0,1 FreeBSD
Quantify abundances of transcripts from RNA-Seq data
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- BSD2CLAUSE
- Categories
- biology
- Package size
- 1163.9 KiB, 2220.1 KiB installed
Description
Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
In the other systems
The newest version among them is 0.52.0, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/kallisto | 0.52.0,1 newest | none known | - | [email protected] | 2026-10-08 |
| NetBSD | biology/kallisto | 0.51.1 | none known | - | [email protected] | - |
| DragonFly | biology/kallisto | 0.48.0_3,1 | none known | - | [email protected] | - |
| GhostBSD | biology/kallisto | 0.52.0,1 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install kallistoFrom the ports tree:
cd /usr/ports/biology/kallisto/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= kallisto>0:biology/kallistoPackages
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 | 0.52.0,1 | 0.52.0,1 | - | - | - |
| FreeBSD:14:quarterly | 0.52.0,1 | 0.52.0,1 | n/a | - | - |
| FreeBSD:15:latest | 0.52.0,1 | 0.52.0,1 | n/a | - | - |
| FreeBSD:15:quarterly | 0.52.0,1 | 0.52.0,1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 0.52.0,1 | 0.52.0,1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
As this port's Makefile names them.
Library 3
libhdf5.so: science/hdf5libsz.so: science/libaeclibhts.so: biology/htslib
The full lists below include those, and their dependencies in turn.
Build dependencies 27
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/htslib
- devel/binutils
- devel/cmake-core
- devel/gettext-runtime
- devel/gmake
- devel/jsoncpp
- devel/libunistring
- devel/libuv
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/gcc14
- math/gmp
- math/mpc
- math/mpfr
- ports-mgmt/pkg
- print/indexinfo
- science/hdf5
- science/libaec
- security/libssh2
- security/rhash
- textproc/expat2
- www/libnghttp2
Run dependencies 19
Required by 2
Configuration
Options name: biology_kallisto
| Option | Default | Description |
|---|---|---|
| EXAMPLES | off | Build and/or install examples |
- USES
- cmake:noninja compiler:c++11-lang gmake localbase:ldflags
- Service scripts
- none
Message after installing
===> NOTICE: The kallisto 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
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| pachterlab-kallisto-v0.52.0_GH0.tar.gz | 5.961651e+06 | 68184e41706d77e409f05a598a87dacdf3cf227f18c028175e2bce8b284bdea4 |