The Intergalactic Utilities Commission was organising it's first hackathon with the aim to make more tools collection aware.
The IUC was available for two days in a Hangout to answers questions and to work together with the Galaxy community to enhance our tools and the overall Galaxy ecosystem. Scientiests from three different continents participated in this and made it a very nice experience and a success story, which the IUC would like to repeat more often.
In the following a list of contributions:
Tools:
- Swap all repeats to multiple='True' where appropriate by @erasche
- Make bedtools annotate collection aware: galaxyproject/tools-iuc#282
- Add collection support to deepTools: https://github.com/fidelram/deepTools/commit/3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6
- Add support for FASTQ R1/R2 pairs using dataset collections from @pjbriggs: https://github.com/fls-bioinformatics-core/galaxy-tools/commit/5de7f4ba384afb0a67b89c01f6884288b48ab8cf
- Make bamtools_split output a dataset collection by @pvanheus and collegues: galaxyproject/tools-devteam#227
- Trim Galore update to use and produce collections: bgruening/galaxytools#245
- Most of the unix text processing tools should be collection ready: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing
- @mr-c worked on the khmer wrappers to accept and produce collections: galaxyproject/tools-iuc#80
- To replace most of the repeat parameters we actually needed support for min/max attributes in the multiple data input parameter, which was implemented in Galaxy by @jmchilton galaxyproject/galaxy#765.
- @mr-c described more of Galaxy's new collection features in the tool XSD project galaxyproject/Galaxy-XSD#4 which was integrated in planemo
- @jmchilton made significant progress toward allowing a multiple data parameter to reduce many collections simultaneously galaxyproject/galaxy#805. This will greatly simplify wrappers such as cuffmerge which includes a confusing repeat for supplying additional dataset lists beyond the first.
@pvanheus wrote a nice summary about his experience during the IUC hackathon and data collections in his blog titled "Adventures in Galaxy output collections".
We hope you all will enjoy the outcome of this hackathon and hope to see you at our next hackathon, stay tuned.
I would include the following links.
@mr-c described more of Galaxy's new collection features in the tool XSD project galaxyproject/Galaxy-XSD#4.
@jmchilton made significant progress toward allowing a multiple data parameter to reduce many collections simultaneously galaxyproject/galaxy#805. This will greatly simplify wrappers such as cuffmerge which includes a confusing repeat for supplying additional dataset lists beyond the first.