recipe rpsbproc

RpsbProc, the post-RPSBLAST Processing Utility.

Homepage:

https://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/README

License:

Public Domain

Recipe:

/rpsbproc/meta.yaml

Links:

doi: 10.1002/cpbi.90

The rpsbproc command line utility is an addition to the standalone version of Reverse Position-Specific BLAST (RPS-BLAST), also known as CD-Search (Conserved Domain Search).

It post-processes the results of local RPS-BLAST searches in order to provide a non-redundant view of the search results, and to provide additional annotation on query sequences, such as domain superfamilies and functional sites, similar to the annotation provided by the corresponding web services (e.g., the NCBI Batch CD-Search web service at http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi).

Specifically, the rpsbproc utility reads the output of rpsblast/rpstblastn, fills in domain superfamily and functional site information for each region of the sequence, re-sorts the hits by a different standard, and calculates a set of non-redundent representative hits. In this way, it turns the raw alignments into domain/site annotations on the query sequence at different redundancy level, basically produce the same data as web-based Batch CD-Search service does. The annotation data is presented in tab-delimited tables to be processed either programatically or manually with a spreadsheet (see details below).

See the CDD and CD-Search help document for additional details about superfamilies, conserved sites, and more:

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml

package rpsbproc

versions:

0.5.0-2,  0.5.0-1,  0.5.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc:

>=13

depends libsqlite:

>=3.47.2,<4.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

linux-aarch64

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 rpsbproc

and update with::

   mamba update rpsbproc

To create a new environment, run:

mamba create --name myenvname rpsbproc

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/rpsbproc:<tag>

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

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