- recipe pasa
PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
- Homepage:
- Documentation:
- License:
BSD / BSD-3-Clause
- Recipe:
- Links:
biotools: PASA, doi: 10.1093/nar/gkg770, doi: 10.1186/gb-2008-9-1-r7
- package pasa¶
- Versions:
2.5.3-2,2.5.3-1,2.5.3-0,2.5.2-3,2.5.2-2,2.5.2-1,2.5.2-0,2.4.1-1,2.4.1-0,2.5.3-2,2.5.3-1,2.5.3-0,2.5.2-3,2.5.2-2,2.5.2-1,2.5.2-0,2.4.1-1,2.4.1-0,2.3.3-2,2.3.3-1,2.3.3-0- Depends:
on cdbtools
on fasta3
>=36.3.8ion gmap
>=2023.10.10on libgcc
>=13on libstdcxx
>=13on lighttpd
on minimap2
>=2.22on pblat
>=2.5on perl
on perl-cgi
on perl-db_file
on perl-dbd-sqlite
on perl-uri
on r-base
on samtools
on slclust
on transdecoder
on ucsc-blat
- 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 pasa
to add into an existing workspace instead, run:
pixi add pasa
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 pasa
Alternatively, to install into a new environment, run:
conda create -n envname pasa
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/pasa:<tag>
(see pasa/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¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pasa/README.html)
