recipe fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data.

Homepage:

https://github.com/ndaniel/fusioncatcher

License:

GPL / GPL-3.0

Recipe:

/fusioncatcher/meta.yaml

Links:

doi: 10.1101/011650

package fusioncatcher

(downloads) docker_fusioncatcher

versions:
1.33-4,  1.33-3,  1.33-2,  1.33-1,  1.33-0,  1.30-1,  1.30-0,  1.20-2,  1.20-1, 

1.33-4,  1.33-3,  1.33-2,  1.33-1,  1.33-0,  1.30-1,  1.30-0,  1.20-2,  1.20-1,  1.20-0,  1.10-3,  1.10-2,  1.10-0,  1.00-1,  1.00-0

depends bbmap:

38.44.*

depends biopython:

>=1.50

depends blat:

35.*

depends bowtie:

1.2.3.*

depends bowtie2:

2.3.5.*

depends bwa:

0.7.12.*

depends coreutils:

depends fastqtk:

depends fusioncatcher-seqtk:

1.2.*

depends grep:

depends gzip:

depends lzo:

depends lzop:

depends numpy:

1.13.1.*

depends oases:

depends openjdk:

depends openpyxl:

2.5.0a2.*

depends parallel:

20171222.*

depends picard:

2.10.6.*

depends pigz:

2.3.*

depends python:

<3

depends samtools:

0.1.19.*

depends sra-tools:

2.9.6.*

depends star:

2.7.2b.*

depends tbb:

2020.2.*

depends ucsc-fatotwobit:

depends ucsc-liftover:

depends velvet:

1.2.10.*

depends xlrd:

1.0.0.*

depends zip:

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 fusioncatcher

and update with::

   mamba update fusioncatcher

To create a new environment, run:

mamba create --name myenvname fusioncatcher

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/fusioncatcher:<tag>

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

Notes

download-human-db.sh should be updated when new version of FusionCatcher is released.

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Render an install-with-bioconda badge with the following MarkDown:

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