- recipe polap
POLAP: plant organelle long-read assembly pipeline
- Homepage:
- Documentation:
- License:
GPL / GPL-3.0-or-later
- Recipe:
- package polap¶
- Versions:
0.5.3.1-0,0.4.3.7.9-0,0.4.3.7.8-0,0.4.3.7.7-0,0.4.3.7.6-1,0.4.3.7.6-0,0.4.3.7.5-3,0.4.3.7.5-1,0.4.3.7.5-0,0.5.3.1-0,0.4.3.7.9-0,0.4.3.7.8-0,0.4.3.7.7-0,0.4.3.7.6-1,0.4.3.7.6-0,0.4.3.7.5-3,0.4.3.7.5-1,0.4.3.7.5-0,0.4.3.7.4-0,0.4.3.7.3-0,0.4.3.7.2-0,0.4.3.7-1,0.4.3.7-0,0.4.1.1-0,0.3.7.3-1,0.3.7.3-0,0.3.7.2-0,0.3.7.1-0,0.3.7-1,0.3.7-0,0.2.6-0,0.2.4-0- Depends:
on assembly-stats
on bedtools
on bioawk
on bioconductor-biostrings
on bioconductor-ggtree
on blast
on clustalw
on csvtk
on entrez-direct
on flye
>=2.9.6on getorganelle
on gfastats
on gfatools
on icu
on kmer-jellyfish
on libxml2
on mafft
on minimap2
>=2.28on networkx
on newick_utils
on orthofinder
on pandas
on pandoc
on parallel
on perl
on perl-xml-libxml
on progressivemauve
on python
>=3.12,<3.13.0a0on r-base
on r-dplyr
on r-optparse
on r-readr
on r-rgbif
on r-stringr
on r-taxize
on r-tidyr
on samtools
on seqkit
on seqtk
on sra-tools
- 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 polap
to add into an existing workspace instead, run:
pixi add polap
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 polap
Alternatively, to install into a new environment, run:
conda create -n envname polap
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/polap:<tag>
(see polap/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/polap/README.html)
