iimog/biom-conversion-server repository overview

⁠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

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

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• Docker

⁠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