todo list for v1 of workshop

[max-mapper]

• hosting infrastructure (@mafintosh)
• docker inside docker (bundling needed images etc) (@mafintosh)
• finish markdown content (@maxogden)
• come up with a data processing use case
• create a gasket pipeline for brunos pipeline (@bmpvieira)
• docker image with samtools in it so we can use samtools tview to view the reads (@pkafei)
• in browser workshop ui (@mafintosh, @maxogden)

[max-mapper]

[max-mapper]

from @bmpvieira on IRC:

7:11 AM <bmpvieira> I haven't finished the stuff for the workshop but I expect to finish it tomorrow
7:11 AM <bmpvieira> my idea was to use bionode-ncbi to get some metadata from ncbi to data
7:12 AM <bmpvieira> like all genomes for for something, bacteria whatever. Then subset that into another dat, like just pick one or two small genomes
7:12 AM <bmpvieira> use a bionode/gasket pipeline to download the reference genome, reads, align the reads to the reference genome and find variants
7:13 AM <bmpvieira> and the last step would be a R analysis/stats/plot inside a docker container
7:14 AM <bmpvieira> I'm trying to keep things simple but also try to showoff a bit of what you can do with dat/bionode/gasket/docker
7:16 AM <bmpvieira> we can also mention or link to examples of some more complex usage like forks and concurrency in a pipeline just in case more skilled participants want to explore that
7:18 AM <bmpvieira> once I finish it tomorrow I'll push everything to github and we can then better discuss/improve it
7:18 AM <bmpvieira> sounds good?

[max-mapper]

@mafintosh @bmpvieira @pkafei let's do a google hangout to discuss ASAP, so we can all know what we need to finish for the workshop

also @bmpvieira i dunno if I mentioned but @pkafei will be joining us in london, but @mafintosh won't be (he is going to australia instead)

time zones are hard, but 8AM for me and @mafintosh (tokyo) is midnight for @bmpvieira (london) which is 4pm for @pkafei (portland). does that time in ~21 hours from now work for everyone? http://everytimezone.com/#2014-10-18,660,cn3

[pkafei]

4pm PST works for me.

[mafintosh]

works for me also

[bmpvieira]

me too

[max-mapper]

OK sweet I will invite you all to a google hangout at the time linked above

[max-mapper]

notes from our hangout:

#8
http://workshop.mathiasbuus.eu/
https://github.com/maxogden/get-dat
http://dat-ncbi-arthropods-summary.inb.io
http://dat-summary.inb.io
https://gist.github.com/bmpvieira/e40835676c086d3f92c4
https://github.com/mafintosh/docker-browser-screenshot
http://genome.sph.umich.edu/wiki/QPLOT
http://www.bioconductor.org/
http://www.bioconductor.org/help/course-materials/2012/CSC2012/Bioconductor-tutorial.pdf
http://en.wikipedia.org/wiki/Variant_Call_Format
http://www.broadinstitute.org/igv/viewing_vcf_files
http://ics.hutton.ac.uk/tablet/
https://pythonhosted.org/rpy2-bioconductor-extensions/
https://raw.githubusercontent.com/ecerami/samtools_primer/master/figs/tview.png
https://github.com/ecerami/samtools_primer
https://github.com/bionode/bionode-sam
https://github.com/bionode/bionode
https://www.npmjs.org/package/bionode-sam
https://github.com/bionode/bionode-sam/blob/master/sam/build.sh
http://www.nature.com/nature/journal/v475/n7357/images_article/nature10231-f2.2.jpg
http://www.nature.com/srep/2011/110706/srep00032/images/srep00032-f3.jpg
http://biobits.org/samtools_primer.html
http://www.cureffi.org/2012/10/17/descriptive-statistics-and-quality-control-on-variants/
http://biobits.org/samtools_primer.html#VisualizingReads
https://gist.github.com/bmpvieira/e40835676c086d3f92c4
samtools view -q 42 -c alignments/sim_reads_aligned.bam
http://samtools.sourceforge.net/tview.shtml
http://samtools.sourceforge.net/mpileup.shtml
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
http://www.broadinstitute.org/igv/AlignmentData
#8
https://github.com/ecerami/samtools_primer
http://www.htslib.org/doc/samtools-1.1.html
https://registry.hub.docker.com/u/sjackman/samtools/
http://try.bionode.io
http://lnug.org

[max-mapper]

I started a new repo for the workshop browser UI: https://github.com/maxogden/adventure-time

[max-mapper]

@bmpvieira and others:

I now have the workshop UI basics hooked up. Me and @mafintosh still have work to do but it's manageable.

The content in the top right pane is being served from this repo (get-dat). I'll rewrite the content to match the new flow as soon as @bmpvieira finishes his parts

[syzer]

its awesome!

[rukku]

That geospatial example looks great. 😄 Will it be part of the tutorial soon?