recipe mimseq

Modification-induced misincorporation tRNA sequencing.

Homepage:

https://github.com/nedialkova-lab/mim-tRNAseq

License:

GPL3 / GPL-3.0-only

Recipe:

/mimseq/meta.yaml

package mimseq

versions:

1.3.8-0,  1.3.7-0,  1.3.6-1,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3-0, 

1.3.8-0,  1.3.7-0,  1.3.6-1,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3-0,  1.2.1-0,  1.2-0,  1.1.7-0,  1.1.6-0,  1.1.4-0,  1.1.2-0,  1.1.1-0,  1.1-0,  1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0-0,  0.4-0,  0.3.4.9-0,  0.3.4.8-0,  0.3.4.7-0,  0.3.4.5-0,  0.3.4.3-0,  0.3.4.1-0,  0.3.4-0,  0.3.3.2-0,  0.3.3-0,  0.3.2-0,  0.3.1-0,  0.2.6-0,  0.2.5.6-0,  0.2.5.5-1,  0.2.5.5-0,  0.2.5.4-0,  0.2.5.3-0

depends bedtools:

>=2.30.0

depends bioconductor-complexheatmap:

>=2.2.0

depends bioconductor-deseq2:

>=1.26.0

depends biopython:

>=1.79

depends blast:

>=2.10.1

depends gmap:

<=2019.02.26

depends infernal:

>=1.1.4

depends matplotlib-base:

>=3.4.2

depends numpy:

>=1.21.1

depends pandas:

>=1.3.1

depends pybedtools:

>=0.8.2

depends pyfiglet:

>=0.8.post1

depends pysam:

>=0.16.0.1

depends python:

3.7.*

depends r-base:

>=4.1

depends r-calibrate:

>=1.7.7

depends r-devtools:

>=2.4.1

depends r-dplyr:

>=1.0.6

depends r-ggplot2:

>=3.3.5

depends r-ggpol:

>=0.0.7

depends r-gridextra:

>=2.3

depends r-pheatmap:

>=1.0.12

depends r-plyr:

>=1.8.6

depends r-reshape2:

>=1.4.4

depends r-tidyverse:

>=1.3.0

depends requests:

>=2.26.0

depends samtools:

>=1.11

depends seaborn-base:

>=0.11.1

depends statsmodels:

>=0.13.1

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 mimseq

and update with::

   mamba update mimseq

To create a new environment, run:

mamba create --name myenvname mimseq

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/mimseq:<tag>

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

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