recipe squire

Quantitative, locus-specific view of transposable element expression.

Homepage:

https://github.com/wyang17/SQuIRE

License:

GNU

Recipe:

/squire/meta.yaml

package squire

versions:

0.9.9.92-1,  0.9.9.92-0

depends bedtools:

2.25.0

depends bioconductor-biocparallel:

1.12.0

depends bioconductor-deseq2:

1.16.1

depends bioconductor-vsn:

depends igvtools:

2.3.93

depends pyfaidx:

depends python:

2.7.*

depends r-base:

3.4.1

depends r-ggrepel:

depends r-hexbin:

depends r-pheatmap:

depends samtools:

1.1

depends star:

2.5.3a

depends stringtie:

1.3.3

depends ucsc-bedgraphtobigwig:

depends ucsc-genepredtobed:

depends ucsc-genepredtogtf:

depends ucsc-gtftogenepred:

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 squire

and update with::

   mamba update squire

To create a new environment, run:

mamba create --name myenvname squire

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/squire:<tag>

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

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