recipe djinn

Convert your linked-read data between formats, almost like magic.

Homepage:

https://github.com/pdimens/djinn

Documentation:

https://pdimens.github.io/djinn

License:

GPL3 / GPL-3.0-or-later

Recipe:

/djinn/meta.yaml

There are disagreements between formats for linked-read data. Haplotagging thinks linked-read barcodes and FASTQ files should look one way, stLFR a different way, and TELLseq yet another. Djinn lets you convert to a standard format, convert between these FASTQ formats, barcode styles, etc. It also provides a convenient method to upload linked-read data to NCBI that preserves barcode information.

package djinn

versions:

1.0.1-0,  1.0-0

depends click:

>=8.2

depends pysam:

>=0.23

depends python:

>=3.11

depends rich-click:

1.9.*

depends samtools:

>=1.22

requirements:

additional platforms:

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 djinn

and update with::

   mamba update djinn

To create a new environment, run:

mamba create --name myenvname djinn

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/djinn:<tag>

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

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