-
recipe
reparation_blast¶ 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.
- Homepage
- License
GPL3
- Recipe
-
package
reparation_blast¶ 
- Versions
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 blast
>=2.7.1
- Depends glimmer
- Depends perl
>=5.26.2,<5.26.3.0a0
- Depends perl-bioperl
>=1.7.2
- Depends perl-posix
- Depends plastid
- Depends prodigal
- Depends pysam
0.14.1.*
- Depends r-ggplot2
>=3.0
- Depends r-prroc
>=1.3.1
- Depends r-randomforest
- Depends r-rocr
- Depends r-sizer
- Depends samtools
- Requirements
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install reparation_blast
and update with:
conda update reparation_blast
or use the docker container:
docker pull quay.io/biocontainers/reparation_blast:<tag>
(see reparation_blast/tags for valid values for
<tag>)
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/reparation_blast/README.html)