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

(downloads) docker_rpsbproc

Versions:

0.5.1-0,  0.5.0-3,  0.5.0-2,  0.5.0-1,  0.5.0-0

Depends:

  • on bzip2 >=1.0.8,<2.0a0

  • on libgcc >=13

  • on libsqlite >=3.51.2,<4.0a0

  • on libstdcxx >=13

  • on libzlib >=1.3.1,<2.0a0

Additional platforms:
linux-aarch64,  osx-arm64

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 rpsbproc

to add into an existing workspace instead, run:

pixi add rpsbproc

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 rpsbproc

Alternatively, to install into a new environment, run:

conda create -n envname rpsbproc

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/rpsbproc:<tag>

(see rpsbproc/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.

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