rockyb/bpwrapper repository overview

⁠Overview

Here we have command-line utilities for popular Bio::Perl⁠ classes.

Specifically:

• bioaln⁠: Bio::SimpleAlign⁠ with additional methods
• biopop⁠: Bio::PopGen⁠ which can be converted from Bio::SimpleAlign; and additional methods
• bioseq⁠: Bio::Seq⁠ with additional methods
• biotree⁠: Bio::Tree⁠ with additional methods

The motivation is to allow users to perform routine BioPerl manipulations of sequences, alignments, and trees without having to write full-blown scripts. For common operations of sequences and alignments, Bio::BPWrapper makes it easy to create workflows with a single BASH script containing a combination command-line calls: no Perl or BioPerl coding is necessary.

Internally, the programs follow a "Wrap, don't Write" design principle. That is, we have full faith in the robustness of the BioPerl development framework. As such, methods here should all be wrappers to BioPerl methods so that exceptions can be handled properly by BioPerl.

The Bio::BPWrapper module also include some useful methods which are not part of Bio::Perl.

⁠Using the docker image

To download the image so that docker recognizes it:

docker pull rockyb/bpwrapper

For things other than getting help, you'll often need to pass a data in file to the program. Do that by sharing the directory that the file is in on the docker invocation.

You'll need to pay attention to the permissions on the data file its directory. The docker container runs as as a user that may not have access to data. I've found however that if you put the data in /tmp files will be seen inside the running docker container.

For example:

$ cp test-data/cds.fas /tmp/cds.fas
$ docker run -it -v /tmp:/test-files rockyb/bpwrapper bioseq -l /test-files/cds.fas
DK2	120
W70332	120
M1608	108
F2

⁠Developers, Contact, Citation

• Yözen Hernández
• Pedro Pagan
• Girish Ramrattan
• Weigang Qiu, City University of New York, Hunter College (Correspondence: [email protected])⁠)
• If you find the tools useful, please cite: Hernadez, Bernstein, et al (2018). BpWrapper::BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Genomics 19:76. Paper link⁠.