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:

https://github.com/PASApipeline/PASApipeline

Documentation:

https://github.com/PASApipeline/PASApipeline/wiki

License:

BSD / BSD-3-Clause

Recipe:

/pasa/meta.yaml

Links:

biotools: PASA, doi: 10.1093/nar/gkg770, doi: 10.1186/gb-2008-9-1-r7

package pasa

versions:

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, 

2.5.3-1,  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 cdbtools:

depends fasta3:

>=36.3.8i

depends gmap:

>=2023.10.10

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends lighttpd:

depends minimap2:

>=2.22

depends pblat:

>=2.5

depends perl:

depends perl-cgi:

depends perl-db_file:

depends perl-dbd-sqlite:

depends perl-uri:

depends r-base:

depends samtools:

depends slclust:

depends transdecoder:

depends ucsc-blat:

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 pasa

and update with::

   mamba update pasa

To create a new environment, run:

mamba create --name myenvname pasa

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/pasa:<tag>

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

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