[galaxy-dev] GCCBOSC 2018 Abstract Submission & Early Registration are Open

[Dave Clements]

Hello all,

We are pleased to announce that abstract submission and early registration
for GCCBOSC2018  are now open.

   - Submit an abstract
    (oral presentation
   abstracts due March 16)
   - Register 
   - Book conference housing 

GCCBOSC 2018  will be held 25-30 June in
Portland, Oregon, United States. This brings the 2018 Galaxy Community
Conference and the Bioinformatics Open Source Conference together into a
unified week-long event. If you work in open source life science or
data-intensive biomedical research, then there is no better place than
GCCBOSC 2018 to present your work and to learn from others.

Events

GCCBOSC  starts with two days of training
 with a
wide range of topics nominated and selected by our communities. Training is
followed by a two day meeting, with joint and parallel tracks, featuring
oral presentations, posters, demos, lightning talks,
birds-of-a-feather and invited
keynotes from Fernando
Pérez

 of the Berkeley Institute for Data Science  and
 Project Jupyter , and Tracy K. Teal

 of The Carpentries. The week finishes with *CollaborationFest
 Core* and
*Encore*, two or four days of collaborative work on code, documentation,
training and challenging data analysis problems.

Abstract Submission

BOSC and GCC are now accepting abstracts
 for oral
presentations, posters, demos, and lightning talks. We are using EasyChair
 for submissions. If you don't already have an
account, you'll need to create one.

*The deadline for oral presentations is rapidly approaching (March 16) so
plan to submit your abstracts soon.*

Registration

Register now  to take full advantage of
 early registration discounts
 for
students/post-docs (75% off full price), non-profits (67%) and industry
(50%). Early registration rates for students and post-docs average $66 /
day.

Conference Housing

Official conference housing  for
GCCBOSC 2018 is in Reed residence halls. Rooms are within easy walking
distance of all conference venues. Room prices per night drop the longer
the stay. If you prefer to stay elsewhere, Reed College has a list of
recommended hotels , many
offering a discount for those attending events at Reed.

Travel Fellowships

Both OBF and the Galaxy Community Fund Board are offering fellowships to
attend GCCBOSC 2018:

   - OBF Travel Fellowships
   ,
   deadline is April 15.
   - GCC2018 Fellowships
   , first
   deadline is March 16.


See you in Portland!

The GCCBOSC 2018 Organizers




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[galaxy-dev] Help with from_dataset param in Galaxy XML

[SAPET, Frederic]

Hello

I try to use the from_dataset param.
I have a tabular file with two columns : sequence and ids

I would like to let users select some sequences, based on the ids.









But I would like to be able to access not only the sequences data, but also the 
ids.
In the   tag :
name=$seq.name : it give me "seq", the name of my parameter
value=$seq.value : it gives me "atcgatcga,tagctacgatcg,aatctactacta", that's 
fine.

I would like to print the id of each sequence.
Is it possible ?

Thank you.

Fred

---
Frederic Sapet
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Centre de Recherche de Chappes
CS 90126
63720 CHAPPES
FRANCE
Tel : +33 (0)4 73 67 88 54
Fax : +33 (0)4 73 67 88 99
E-mail : frederic.sa...@biogemma.com

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Re: [galaxy-dev] bigwig problem

[Jochen Bick]

Thanks, nate,

can you tell me one I can update? And what i need to update?

Cheers Jochen

On 15.02.2018 16:24, Nate Coraor wrote:
> Hi Jochen,
> 
> I ran in to this yesterday, we're working on fixing it right now. It's due
> to this:
> 
> https://github.com/bioconda/bioconda-recipes/issues/5430
> 
> And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage,
> which still points to the old versions. I have an update here:
> 
> https://github.com/galaxyproject/conda-iuc/pull/14
> 
> Once that is available you should be able to `conda update ucsc_tools` the
> affected environments. I am also working on switching all of the
> requirements so they depend on the individual ucsc-* packages from Bioconda
> instead of the metapackage so we shouldn't need to maintain it in the
> future.
> 
> --nate
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