- recipe jaffa
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts then searches for gene fusions. This package contains the wrappers jaffa-direct, jaffa-assembly, and jaffa-hybrid. You can pass the "refSeq" parameter in the environment variables JAFFA_REF_BASE. Otherwise, pass any paramters to the wrappers as you would to the bpipe JAFFA_{method} call in the manual.
- Homepage:
- License:
GPL-3.0-or-later
- Recipe:
- package jaffa¶
- Versions:
2.5-0,2.3-0,2.2-0,2.1-0,2.00-1,2.00-0,1.09-2,1.09-1,1.09-0,2.5-0,2.3-0,2.2-0,2.1-0,2.00-1,2.00-0,1.09-2,1.09-1,1.09-0,1.08-0- Depends:
on bbmap
on bioconductor-iranges
on bowtie2
on bpipe
on fastx_toolkit
on oases
on samtools
1.1on trimmomatic
on ucsc-blat
on velvet
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install jaffa
to add into an existing workspace instead, run:
pixi add jaffa
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install jaffa
Alternatively, to install into a new environment, run:
conda create -n envname jaffa
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/jaffa:<tag>
(see jaffa/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
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