recipe salmon

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment.

Homepage:

https://github.com/COMBINE-lab/salmon

Documentation:

https://combine-lab.github.io/salmon

License:

GPL3 / GPL-3.0-or-later

Recipe:

/salmon/meta.yaml

Links:

biotools: salmon, usegalaxy-eu: salmon, usegalaxy-eu: salmonquantmerge, usegalaxy-eu: alevin, doi: 10.1038/nmeth.4197

package salmon

versions:

1.10.3-4,  1.10.3-3,  1.10.3-2,  1.10.3-1,  1.10.3-0,  1.10.2-0,  1.10.1-2,  1.10.1-1,  1.10.1-0, 

1.10.3-4,  1.10.3-3,  1.10.3-2,  1.10.3-1,  1.10.3-0,  1.10.2-0,  1.10.1-2,  1.10.1-1,  1.10.1-0,  1.10.0-0,  1.9.0-1,  1.9.0-0,  1.8.0-1,  1.8.0-0,  1.7.0-1,  1.7.0-0,  1.6.0-0,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.0-1,  1.4.0-0,  1.3.0-0,  1.2.1-0,  1.2.0-0,  1.1.0-0,  1.0.0-0,  0.15.0-0,  0.14.2-1,  0.14.2-0,  0.14.1-2,  0.14.1-1,  0.14.1-0,  0.14.0-1,  0.14.0-0,  0.13.1-0,  0.13.0-2,  0.13.0-1,  0.12.0-1,  0.11.3-2,  0.11.3-1,  0.11.2-0,  0.11.1-0,  0.11.0-0,  0.10.2-3,  0.10.2-1,  0.10.1-1,  0.10.0-1,  0.9.1-1,  0.9.1-0,  0.9.0-0,  0.8.2-1,  0.8.2-0,  0.8.1-0,  0.8.0-0,  0.7.2-3,  0.7.2-2,  0.6.0-2,  0.6.0-1,  0.6.0-0,  0.5.1-0

depends boost-cpp:

depends bzip2:

>=1.0.8,<2.0a0

depends icu:

depends libcurl:

>=8.12.1,<9.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends libgff:

>=2.0.0,<3.0a0

depends libiconv:

>=1.18,<2.0a0

depends libjemalloc:

>=5.3.0

depends liblzma:

>=5.6.4,<6.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends staden_io_lib:

>=1.15.0

depends staden_io_lib:

>=1.15.0,<2.0a0

depends tbb:

>=2022.0.0

depends zstd:

>=1.5.7,<1.6.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install salmon

and update with::

   mamba update salmon

To create a new environment, run:

mamba create --name myenvname salmon

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/salmon:<tag>

(see `salmon/tags`_ for valid values for ``<tag>``)

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