GCC 2017 has ended
The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

The full printed program is also available.
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Thursday, June 29 • 15:40 - 17:00
P11: Utility scripts for data manipulation in Galaxy

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Poster (doi: 10.7490/f1000research.1114416.1)


Simon Gladman 1*, Madison Flannery 1
1 : Melbourne Bioinformatics, The University of Melbourne  (MelBioinfo), Victoria, Australia
* : Corresponding author

Galaxy has an excellent system for the storage, indexing and handling of large sets of reference genome data that are required by various tools. This works particularly well for eukaryotic genomes such as human and mouse etc. However, in the case of micro-organisms there are many thousands of reference genomes. These genomes are quite small and so are very easily indexed on the fly as required. We have developed a set of utility scripts to take bacterial genomes and build galaxy data libraries of them by genus and/or species. The data libraries can be created on a local or remote machine easily. The utility scripts are also capable of taking an arbitrary directory structure and creating data libraries based upon on them.

The second script - galaxy-fuse - is a file system creation script that makes the Galaxy histories of a particular user available on the local file system in a matching directory structure. It uses the Galaxy user's api and bio-blend access to the Galaxy database to name the files. 

This poster describes the rationale, development and distribution of the two tools.

avatar for Simon Gladman

Simon Gladman

University of Melbourne

Thursday June 29, 2017 15:40 - 17:00 CEST
Le Corum Le Corum

Attendees (5)