- recipe secapr
Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing.
- Homepage:
- License:
MIT
- Recipe:
- package secapr¶
- versions:
2.2.8-0,2.2.6-0,2.2.5-0,2.2.4-0,2.2.3-0,2.2.1-0,2.1.1-0,2.1.0-0,2.0.3-0,2.2.8-0,2.2.6-0,2.2.5-0,2.2.4-0,2.2.3-0,2.2.1-0,2.1.1-0,2.1.0-0,2.0.3-0,2.0.2-0,1.1.15-2,1.1.15-1,1.1.15-0,1.1.14-0,1.1.12-0,1.1.10-2,1.1.10-0,1.1.9-0,1.1.8-0,1.1.7-0,1.1.4-0,1.1.0-0,1.0.2-0,1.0.1-0- depends abyss:
- depends biopython:
- depends blast:
- depends bwa:
- depends emboss:
- depends fastqc:
- depends mafft:
- depends matplotlib-base:
- depends muscle:
- depends pandas:
- depends python:
- depends samtools:
1.9.*- depends spades:
- depends trimal:
- depends trimmomatic:
- 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 secapr and update with:: mamba update secapr
To create a new environment, run:
mamba create --name myenvname secapr
with
myenvnamebeing 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/secapr:<tag> (see `secapr/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/secapr/README.html)
