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biom-conversion-server

A simple php server that can convert biom version 2 (hdf5) files and data to biom version 1 (json) and vice versa. It simply provides a web and API interface to the convert feature of the official python biom format tool. This project is not part of the official biom project.

Please cite our article at f1000 Research that describes this module:

Markus J. Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, and Alexander Keller.
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format[version 2; referees: 1 approved, 2 approved with reservations].
F1000Research 2017, 5:2348. doi: 10.12688/f1000research.9618.2

You can cite the current version of this software repository using the Zenodo Zenodo

Please cite the original biom project in addition to this project as:

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.
GigaScience 2012, 1:7. doi:10.1186/2047-217X-1-7

A public instance of the server is running at https://biomcs.iimog.org


  • Cite Project DOI and Zenodo
  • License MIT
  • Build Status Travis
  • Test Coverage Coveralls
  • Code Climate CodeClimate
  • Docker DockerPulls

Getting started

To run your own conversion server on localhost port 8080 using the docker container execute the following commands:

docker pull iimog/biom-conversion-server
# Use any other port by exchanging 8080 with your desired port number
docker run -d --publish 8080:80 --name biomcs iimog/biom-conversion-server

Now you can visit your conversion server in the browser at http://localhost:8080/ And you can point tools that use the conversion api as a webservice to http://localhost:8080/convert.php (e.g. biojs-io-biom).

Changes

1.0.6 (2018-10-04)

  • Update node version in docker container
  • Update required bootstrap version (CVE-2018-14041)

1.0.5 (2018-03-27)

  • Update biom-format to version 2.1.6

1.0.4 (2017-07-28)

  • Switch from bower to yarn
  • Update dependencies
  • Update of biojs-io-biom to version 1.0.9

1.0.3 (2017-03-29)

  • Update of biojs-io-biom to version 1.0.7

1.0.2 (2016-12-22)

  • Fix docker image

1.0.1 (2016-12-22)

  • Update of biojs-io-biom to version 1.0.6

1.0.0 (2016-09-07)

  • Update of biojs-io-biom to version 1.0.1

0.4.0 (2016-09-06)

  • Add details to error messages

0.3.0 (2016-07-29)

  • Use biojs-io-biom for UI
  • Add UI to start page (file upload/download)
  • Increase php server limits

0.2.0 (2016-07-25)

  • returned content is base64 encoded string
  • require content as base64 encoded string
  • handle post data passed as json
  • set correct content-type header
  • allow CORS requests

0.1.0 (2016-07-08)

  • convert to json
  • convert to hdf5
  • docker container
  • integrate testing