recipe seqscreen

SeqScreen was created to sensitively assign taxonomic classifications, functional annotations, and Functions of Sequences of Concern (FunSoCs) to single, short DNA sequences or open reading frames.

Homepage:

https://gitlab.com/treangenlab/seqscreen/-/wikis/home

License:

GPL3

Recipe:

/seqscreen/meta.yaml

package seqscreen

versions:

4.3-0,  4.2-0,  4.1-2,  4.1-1,  4.1-0,  4.0-8,  4.0-7,  4.0-6,  4.0-5, 

4.3-0,  4.2-0,  4.1-2,  4.1-1,  4.1-0,  4.0-8,  4.0-7,  4.0-6,  4.0-5,  4.0-4,  4.0-3,  4.0-2,  4.0-1,  4.0-0,  3.4-0,  3.3-1,  3.3-0,  3.2-0,  3.1-0,  3.0-1,  3.0-0,  2.2-0,  2.1-0,  2.0.2-0,  2.0.1-0,  2.0-1,  2.0-0,  1.6.4-2,  1.6.4-1,  1.6.4-0,  1.6.3-0,  1.6.2-0,  1.6.1-0,  1.6.0-0,  1.5.11-0,  1.5.10-0,  1.5.9-0,  1.5.8-0,  1.5.7-0,  1.5.6-0,  1.5.4-0,  1.5.3-0,  1.5.2-0,  1.5.0-0,  1.4.14-1,  1.4.14-0,  1.4.12-0,  1.4.11-0,  1.4.10-0,  1.4.9-0,  1.4.8-0,  1.4.7-0,  1.4.6-0,  1.4.5-0,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.4.0-1,  1.4.0-0,  1.3.1-0,  1.3.0-1,  1.3.0-0

depends biopython:

depends bitarray:

depends blast:

>=2.10

depends bowtie2:

depends bwa:

0.7.17.*

depends centrifuge-core:

depends diamond:

>=2.0.15

depends ete3:

>=3.1.2

depends gdrive:

depends hmmer:

depends intervaltree:

depends jinja2:

depends minimap2:

>=2.24

depends mmseqs2:

depends mummer:

depends ncbi-datasets-cli:

13.20.1.*

depends nextflow:

21.10.6.*

depends pandas:

>=1.4.3

depends pyfasta:

0.5.2.*

depends python:

>=3

depends rapsearch:

depends samtools:

>=1.15.1

depends scikit-learn:

depends scipy:

depends time:

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 seqscreen

and update with::

   mamba update seqscreen

To create a new environment, run:

mamba create --name myenvname seqscreen

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/seqscreen:<tag>

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

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