The day concluded with 7 minute lightning talks from the Galaxy community. This is a great chance for folks to talk about ideas and implementations that are in progress.
Jessica Kissinger — Enabling Galaxy to access web services
Accessing foreign resources by pointing and clicking. Remote web services are available all over the place: ~1700 on Biocatalogue.
Galaxy integration of web services handles both types of Web Services: REST and SOAP. Universal client access the service WADL file to determine which calls can be made and what parameters are needed. SOAP implementation required adding a web service creator tool: dynamically populates Galaxy’s tool panel with available services and populates parameters from WSDL description file.
Future plans are to support ontologies within the web services.
Ry4an Brase — Mercurial for Galaxy Admins
Mercurial is Galaxy’s decentralized source control. Mercurial is delta based that keeps track of a series of changes to your work. Lots of nice, and hilarious, mercurial tips:
Checking for updates:
hg incoming Track your local changes:
hg rename --after your_conf.xml orig_conf.xml.orig Local mercurial server:
Hiding uninteresting complexing from users. Dealing with multi-part datasets — need all items of a dataset to be used; and complex reports which are not normally useful but sometimes needed. Example of multi-part datasets: bed/bim/fam (genotypes/map/pedigree) for SNP genotyping.
An example is in rgenetics.py: a HTML file is generated as the return of the program which has callbacks to the more complex analysis. Keeps all 3 files together in one object. Similarly for complicated outputs, use a HTML file as the output that links everything. It’s one item, and if you need anything can pull from this file.
Asaaf Gordon — Useful and Usable
Some suggestions based on his love of Galaxy:
Bowtie parameters: commonly used — what are they? Full parameter list — a mess of too many; not useful and confusing. Need a subset of parameters that are make it more useful.
Useful data for next gen sequencing: percentages of mapping and non-mapping. Coverage of mapped. List of non-mapped reads. Give back an HTML file with links to summary information, tracks and all of the associated files.
Atsuko Yamaguchi — DBCLS Galaxy: Galaxy in Japanese
Aim to the solve the problem of finding data in individual databases. Lots of different repositories and difficult to know where to get it. Idea is to use DBCLS Galaxy to talk to TogoDB and TogoWS. TogoWS talks to major databases so a centralized place to retrieve information. DBCLS Galaxy provides a place for data sharing and analysis. Development work produced a bootable image with DBCLS Galaxy including tools linked to TogoWS and TogoDB. Also documentation in Japanese.
Mitsuteru Nakao — Galaxy Internationalization and Localization
Internationalization involves displaying non-ascii data, which is partly integrated but not currently working. For localization can change language in browser: uses GNU gettext. Introduce a locale template file with Japanese messages. Problem includes other text such as help information in tools.
Japanese DBCLS server also includes tools for Semantic Web work including SPARQL queries.
Wishlist for using Galaxy on next gen sequencing pipelines. Current pipeline is partially constructed but not fully automated. Use Ibis base caller, an improved base identification system and then a master python script that runs analyses. Would like to move this to Galaxy to keep track of what type of analysis was done and with what parameters.
Available tools from USC for next-gen analysis:
PerM — short read mapping. Uses periodic space seed: no matter where a pair of mismatches occur on the 32mer, there is a shift for which both will be masked so you are not blind to these spaced errors.
Clippers — find novel splice junctions, similar to Tophat. Target for long reads covering one splice junction.
Tade Souaiaia — ComB SNP calling for SOLiD data
ComB is an addition to PerM with SNP calling for SOLiD. This deals with things in color space without converting to base space, which avoids a loss of information. Comparison of ComB with a samtools/maq/bfast approach in base space.