recipe squid

Detector for fusion-gene and non-fusion-gene transcriptomic structural variations from RNA-seq data

Homepage:

https://github.com/Kingsford-Group/squid

License:

BSD 3

Recipe:

/squid/meta.yaml

Links:

doi: 10.1186/s13059-018-1421-5

package squid

versions:

1.5-8,  1.5-7,  1.5-6,  1.5-5,  1.5-4,  1.5-3,  1.5-2,  1.5-1,  1.5-0, 

1.5-8,  1.5-7,  1.5-6,  1.5-5,  1.5-4,  1.5-3,  1.5-2,  1.5-1,  1.5-0,  1.4-0

depends bamtools:

>=2.5.2,<2.6.0a0

depends glpk:

>=5.0,<6.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends zlib:

requirements:

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 squid

and update with::

   mamba update squid

To create a new environment, run:

mamba create --name myenvname squid

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/squid:<tag>

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

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