recipe reparation_blast

A pipeline that detects novel open reading frames with ribseq data for bacteria.

Homepage:

https://github.com/RickGelhausen/REPARATION_blast

License:

GPL3

Recipe:

/reparation_blast/meta.yaml

A pipeline that uses ribosome profiling data for a de novo open reading frame delineation in prokaryotic (bacterial) genomes. I changed the original reparation project to use the open-source blast tool (https://blast.ncbi.nlm.nih.gov/Blast.cgi) instead of the commercial usearch --ublast tool (https://drive5.com/usearch/manual/ublast_algo.html). I did this in order to add this tool to bioconda without having licensing issues with the commercial usearch -ublast tool. The original software was created at VIB-UGent Center for Medical Biotechnology and Lab of Bioinformatics and Computational Genomics (Biobix), University of Gent, Belgium, by Elvis Ndah. (https://github.com/Biobix/REPARATION). Be advised that the adapted version has slightly different results and is slower than the original reparation software.

package reparation_blast

versions:

1.0.9-3,  1.0.9-2,  1.0.9-1,  1.0.9-0,  1.0.8-0,  1.0.7-2,  1.0.7-0,  v1.0.7-1,  v1.0.7-0, 

1.0.9-3,  1.0.9-2,  1.0.9-1,  1.0.9-0,  1.0.8-0,  1.0.7-2,  1.0.7-0,  v1.0.7-1,  v1.0.7-0,  v1.0.6-0,  v1.0.5-0,  v1.0.4-0,  v1.0.3-2,  v1.0.2-1,  v1.0.1-0

depends biopython:

1.77.*

depends blast:

depends glimmer:

depends openssl:

>=1.1.0,<=1.1.1

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-bioperl:

>=1.7.2

depends perl-posix:

depends plastid:

depends prodigal:

depends pysam:

0.16.0.1.*

depends r-ggplot2:

depends r-prroc:

depends r-randomforest:

depends r-rocr:

depends r-sizer:

depends samtools:

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 reparation_blast

and update with::

   mamba update reparation_blast

To create a new environment, run:

mamba create --name myenvname reparation_blast

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/reparation_blast:<tag>

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

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