recipe slamdunk

Slamdunk is a software tool for SLAMseq data analysis.

Homepage:

http://t-neumann.github.io/slamdunk

Documentation:

http://t-neumann.github.io/slamdunk/docs.html

Developer docs:

https://github.com/t-neumann/slamdunk

License:

AGPL / GNU Affero General Public License v3 (AGPLv3)

Recipe:

/slamdunk/meta.yaml

Links:

doi: 10.1186/s12859-019-2849-7

<img src="http://t-neumann.github.io/slamdunk/images/slamdunk_logo_light.png" width="300" title="Slamdunk">

### Streamlining SLAM-Seq analysis with ultra-high sensitivity.

[](https://github.com/t-neumann/slamdunk/releases/latest) [](https://travis-ci.org/t-neumann/slamdunk)

[](https://hub.docker.com/r/tobneu/slamdunk) [](https://hub.docker.com/r/tobneu/slamdunk/builds/)

[](http://bioconda.github.io/recipes/slamdunk/README.html) [](https://anaconda.org/bioconda/slamdunk) [](https://anaconda.org/bioconda/slamdunk)

[](https://pypi.python.org/pypi/slamdunk) 

-----

### Slamdunk documentation

http://t-neumann.github.io/slamdunk

### Please cite

Neumann, T., Herzog, V. A., Muhar, M., Haeseler, von, A., Zuber, J., Ameres, S. L., & Rescheneder, P. (2019). [Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2849-7). BMC Bioinformatics, 20(1), 258. http://doi.org/10.1186/s12859-019-2849-7

package slamdunk

versions:

0.4.3-0,  0.4.2-1,  0.4.2-0,  0.4.1-0,  0.4.0-1,  0.4.0-0,  0.3.4-1,  0.3.4-0,  0.3.3-0, 

0.4.3-0,  0.4.2-1,  0.4.2-0,  0.4.1-0,  0.4.0-1,  0.4.0-0,  0.3.4-1,  0.3.4-0,  0.3.3-0,  0.3.2-1,  0.3.2-0

depends biopython:

>=1.74

depends intervaltree:

>=3.0.2

depends joblib:

>=0.14.0

depends nextgenmap:

0.5.5.*

depends pandas:

>=0.25.3

depends pybedtools:

>=0.8.0

depends python:

>=3

depends r-getopt:

depends r-gridextra:

depends r-matrixstats:

>=0.55.0

depends r-tidyverse:

>=1.3.0

depends samtools:

>=1.9

depends varscan:

2.4.4.*

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 slamdunk

and update with::

   mamba update slamdunk

To create a new environment, run:

mamba create --name myenvname slamdunk

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/slamdunk:<tag>

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

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