aaronrphillips/spocs repository overview

⁠SPOCS

⁠Quickstart

To run spocs via the web interface, launch the container as follows:

docker run -p 3000:3000 aaronrphillips/spocs

Then open your browser to localhost:3000 to view the web interface. After selecting input data and configuring parameters, click Submit to run the SPOCS job in the container. When finished, you will either be redirected to the HTML output, or the text report file will be downloaded (depending on the option selected)

To stop the container, run the following:

docker stop `docker ps | grep aaronrphillips | awk '{print $1}'`

NOTE: You must restart the container before starting a new SPOCS run

⁠Running SPOCS Manually

You can also skip the web interface and run the spocs binary directly. To do this, simply add spocs to the end of your command:

docker run -p 3000:3000 aaronrphillips/spocs spocs <spocs args>

⁠Persisting Data

By default, the web interface allows for downloading of results data, so no volumes need to be mounted. However, in order to run spocs manually you will have to mount at least one volume:

docker run -p 3000:3000 -v `pwd`/host_dir:/data/spocs aaronrphillips/spocs spocs -s /data/spocs/fasta/a.fasta /data/spocs/fasta/b.fasta -p /data/spocs/paralogs -R /data/spocs/report

A few notes:

• In the example above, the directory `pwd`/host_dir on the host would have to have three subdirectories. paralogs/ and report/ should be empty, and fasta/ should contain input data
• When running the web interface, data can be persisted by mounting an empty host directory ( `pwd`/host_dir above) to /data/spocs.
• When running spocs manually the directory can be mounted anywhere, as long as the arguments passed to spocs correspond to the correct location(s).

⁠Using wildcards

Unfortunately, * wildcards are not passed correctly to the spocs binary. This makes specifying input files tedious, since it requires you to list each file out individually (as in the example above). However, to use wildcards, you can wrap your spocs command in a call to /bin/bash:

docker run -p 3000:3000 -v `pwd`/host_dir:/data/spocs aaronrphillips/spocs /bin/bash -c 'spocs -s /data/spocs/fasta/*.fasta ...'

⁠Citations, Disclaimers, and Acknowledgements

To cite this software please use the following citation:

Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA. SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes. Bioinformatics. 2013;29(20):2641-2642. doi:10.1093/bioinformatics/btt454.

DISCLAIMER:

The software and materials was prepared as an account of work by AUTHORS at the Pacific Northwest National Laboratories and sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, APPARATUS, PRODUCT, SOFTWARE, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.

ACKNOWLEDGMENT:

This software and its documentation were produced with United States Government support under Contract Number DE-AC05-76RL01830 awarded by the United States Department of Energy. The United States Government retains a paid-up non-exclusive, irrevocable worldwide license to reproduce, prepare derivative works, perform publicly and display publicly by or for the US Government, including the right to distribute to other US Government contractors.

The newest version of this software and documentation is at: http://cbb.pnnl.gov/portal/tools/spocs.html⁠

Read the INSTALL file for installing the software on your system.