Package Recipe 'logan_blaster'

recipe logan_blaster

Align genomic sequences against Logan contigs or unitigs

Homepage:: https://github.com/pierrepeterlongo/logan_blaster
Documentation:: https://github.com/pierrepeterlongo/logan_blaster/blob/main/README.md
License:: GPL-3.0-only
Recipe:: /logan_blaster/meta.yaml

logan_blaster downloads Logan contigs or unitigs for a list of SRA accessions, recruits sequences sharing k-mers with a query using back_to_sequences, and aligns them against the query with BLAST. It can also process a session ID from the Logan search portal (logan-search.org).

package logan_blaster¶

Versions:

0.1.3-1, 0.1.3-0

Depends:

on back_to_sequences
on blast
on count_logan_tig_coverage
on jq
on python >=3.8
on wget

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 logan_blaster

to add into an existing workspace instead, run:

pixi add logan_blaster

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 logan_blaster

Alternatively, to install into a new environment, run:

conda create -n envname logan_blaster

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/logan_blaster:<tag>

(see logan_blaster/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/logan_blaster/README.html)