BSD Portsbiology/salmon 1.10.3_2 FreeBSD
Transcript-level quantification of RNA-seq from lightweight alignments
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv3
- Categories
- biology
- Package size
- 15623.2 KiB, 118261.5 KiB installed
Description
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/salmon | 1.10.3_2 |
| NetBSD | wip/salmon | 0.11.3 |
| HardenedBSD | biology/salmon | 1.10.3_2 |
| GhostBSD | biology/salmon | 1.10.3_2 |
Install
Binary package:
pkg install salmonFrom the ports tree:
cd /usr/ports/biology/salmon/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= salmon>0:biology/salmonPackages
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 | 1.10.3_2 | 1.10.3_2 | - | - | - |
| FreeBSD:14:quarterly | 1.10.3_2 | 1.10.3_2 | n/a | - | - |
| FreeBSD:15:latest | 1.10.3_2 | 1.10.3_2 | n/a | - | - |
| FreeBSD:15:quarterly | 1.10.3_2 | 1.10.3_2 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.10.3_2 | 1.10.3_2 | 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.
Build 9
bash: shells/bashcereal>=1.3.0: devel/cereallibgff>=2.0.0: biology/libgfflibtool: devel/libtoolautoreconf: devel/autoconfaclocal: devel/automakeeigen>0: math/eigen3libdivide>0: math/libdividecurl>0: ftp/curl
Library 1
libtbb.so: devel/onetbb
The full lists below include those, and their dependencies in turn.
Build dependencies 45
- archivers/brotli
- archivers/liblz4
- archivers/zstd
- biology/libgff
- devel/autoconf
- devel/autoconf-switch
- devel/automake
- devel/binutils
- devel/boost-libs
- devel/cereal
- devel/cmake-core
- devel/gettext-runtime
- devel/gmake
- devel/hwloc2
- devel/icu
- devel/jsoncpp
- devel/level-zero
- devel/libpciaccess
- devel/libtool
- devel/libunistring
- devel/libuv
- devel/m4
- devel/onetbb
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/gcc14
- lang/perl5.42
- math/blas
- math/eigen3
- math/gmp
- math/lapack
- math/libdivide
- math/mpc
- math/mpfr
- misc/hwdata
- ports-mgmt/pkg
- print/indexinfo
- security/libssh2
- security/rhash
- shells/bash
- textproc/expat2
- textproc/libxml2
- www/libnghttp2
Run dependencies 8
No port depends on this one.
Configuration
No options to configure.
- USES
- cmake:noninja gmake localbase shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The salmon 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 4
| File | Size | SHA256 |
|---|---|---|
| COMBINE-lab-salmon-v1.10.3_GH0.tar.gz | 7.193092e+06 | a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871 |
| COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz | 3.368105e+06 | 5d345ba30f22ff4448f4bf2920d2246a11cc38b203e12828c07b2612e41d2951 |
| jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz | 3.381908e+06 | 5fef32bb10991b388b4a92292e58d6ef8e7eda812ab2d6a10daaca9a757e6302 |
| samtools-htscodecs-de42211_GH0.tar.gz | 3.200933e+06 | 65e632bf00e2e456a3040e8a4748dbd33161595029ba49dec89d5301ebdd4de6 |