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Bioconda Contribution Fest: 2-3 November #2277

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bgruening opened this Issue Sep 4, 2016 · 53 comments

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bgruening commented Sep 4, 2016

With all the changes that will come in the next weeks and a few open issues concerning the overall quality of our packages I thought about organizing an online contribution fest. Maybe over one or two days, where we all gather together (online) and work on some specific tasks.

Our first Contribution Fest will be on the 2-3 November! We will have an IRC channel (maybe gitter?) and a google hangout in place.

We will start with a short presentation of all ideas and try to create small groups to tackle problems small groups.
I guess it's a good idea if you fork bioconda-recipes and get your own travis setup up and running so we avoid the travis bottleneck.

Some ideas on what we can work on:

  • more tests: #2276
  • improving documentation
  • getting more packages to build under OSX
  • interest in setting up Windows builds?
  • betting travis testing - fail early! #1860
  • perl/R packages should be migrated into a subdir
  • convert all packages from git_url to url
  • transition generic packages (ex. scala, generic pypi packages) from bioconda to conda-forge
  • Implement security enhancements (e.g. #2327)
  • Perhaps we should set up a doodle poll for a "kickoff" google hangout of 1 hour, something like the opening session of a conference or a meet-and-greet?

Moreover, we have some issue that could be worked on:
https://github.com/bioconda/bioconda-recipes/labels/hackathon

PreHack preparation:

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This is a great idea; I will happily participate to the extent I have time available.

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tomkinsc commented Sep 4, 2016

This is a great idea; I will happily participate to the extent I have time available.

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I'd participate in some capacity.

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jmchilton commented Sep 4, 2016

I'd participate in some capacity.

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Good idea. I may not be able to do things synchronously due to time constraints, but would be happy to participate otherwise.

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daler commented Sep 4, 2016

Good idea. I may not be able to do things synchronously due to time constraints, but would be happy to participate otherwise.

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@daler this could be a chance to see PR all 24h :)

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bgruening commented Sep 4, 2016

@daler this could be a chance to see PR all 24h :)

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What are your specific task ideas so far? In any case, I'd participate.

On Sun, Sep 4, 2016, 7:16 AM Björn Grüning notifications@github.com wrote:

@daler https://github.com/daler this could be a chance to see PR all
24h :)


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brwnj commented Sep 4, 2016

What are your specific task ideas so far? In any case, I'd participate.

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@daler https://github.com/daler this could be a chance to see PR all
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@brwnj I have added a few ideas to the top post.

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bgruening commented Sep 4, 2016

@brwnj I have added a few ideas to the top post.

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Hey, I will also contribute. Especially #1860 sounds interesting for me :-)

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eggzilla commented Sep 4, 2016

Hey, I will also contribute. Especially #1860 sounds interesting for me :-)

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Would be happy to contribute! I think weekends might be easier for me, but
perhaps we should find a consensus time.

On Sun, Sep 4, 2016, 8:09 AM Florian Eggenhofer notifications@github.com
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Hey, I will also contribute. Especially #1860
#1860 sounds
interesting for me :-)


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dkoppstein commented Sep 4, 2016

Would be happy to contribute! I think weekends might be easier for me, but
perhaps we should find a consensus time.

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Hey, I will also contribute. Especially #1860
#1860 sounds
interesting for me :-)


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Hi all, I'm in! 😃

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leobiscassi commented Sep 4, 2016

Hi all, I'm in! 😃

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I will try participate too.

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nturaga commented Sep 4, 2016

I will try participate too.

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I am very pressed for time, but I will try to participate

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tiagoantao commented Sep 5, 2016

I am very pressed for time, but I will try to participate

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Idea:

#2282 (age of packages)

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tiagoantao commented Sep 5, 2016

Idea:

#2282 (age of packages)

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I would be very interested, but it depends on when.

On Sep 5, 2016 4:08 AM, "Tiago Antao" notifications@github.com wrote:

Idea:

#2282 #2282 (age of
packages)


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jerowe commented Sep 5, 2016

I would be very interested, but it depends on when.

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Idea:

#2282 #2282 (age of
packages)


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Same here; interested but depends on date/time.

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cbrueffer commented Sep 5, 2016

Same here; interested but depends on date/time.

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I'm in of course. My time is very limited at the moment, but I'll try to join!!

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johanneskoester commented Sep 5, 2016

I'm in of course. My time is very limited at the moment, but I'll try to join!!

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I am also interested. My contribution depends as well on the time i have available and my knowledge of the bioconda system

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mdehollander commented Sep 5, 2016

I am also interested. My contribution depends as well on the time i have available and my knowledge of the bioconda system

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I am also interested, time and familiarity with the bioconda system
permitting!
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I am also interested. My contribution depends as well on the time i have
available and my knowledge of the bioconda system


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jrderuiter commented Sep 5, 2016

I am also interested, time and familiarity with the bioconda system
permitting!
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I am also interested. My contribution depends as well on the time i have
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bioconda has been a great resource to me. I'd be interested in helping.

Another potential issue to flag, related to #1860 is what to do with packages that were added to bioconda early on but are now upstream. (r-ggplot2, click, others? probably many now). maybe these should be pruned?

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zachcp commented Sep 6, 2016

bioconda has been a great resource to me. I'd be interested in helping.

Another potential issue to flag, related to #1860 is what to do with packages that were added to bioconda early on but are now upstream. (r-ggplot2, click, others? probably many now). maybe these should be pruned?

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Is someone working on upgrading R and Rpy? If so I'll join you. We should make our own TODO-thread for this. I cannot do it alone: someone with a more complete understanding of R, Rpy2, anaconda and its quirks is needed.

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endrebak commented Sep 6, 2016

Is someone working on upgrading R and Rpy? If so I'll join you. We should make our own TODO-thread for this. I cannot do it alone: someone with a more complete understanding of R, Rpy2, anaconda and its quirks is needed.

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I'll try to join if I have time!

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abretaud commented Sep 6, 2016

I'll try to join if I have time!

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This is a great idea!

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lucapinello commented Sep 7, 2016

This is a great idea!

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This is great! I've been wanting to contribute more to bioconda so a sprint
like this would be great!

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This is a great idea!


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olgabot commented Sep 7, 2016

This is great! I've been wanting to contribute more to bioconda so a sprint
like this would be great!

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This is a great idea!


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I'd like to - might be able to join depending on timing.

I'm a bit behind on Bioconda recent changes however, would need to find out what's been happening.

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tseemann commented Sep 8, 2016

I'd like to - might be able to join depending on timing.

I'm a bit behind on Bioconda recent changes however, would need to find out what's been happening.

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Down for helping with this!

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roryk commented Sep 8, 2016

Down for helping with this!

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I might take some time to look at some OS X issues!

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yesimon commented Sep 8, 2016

I might take some time to look at some OS X issues!

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Wow, what a great response! Thanks so much!!!!
What about the 10th and 11th of October - or do we need a doodle?

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bgruening commented Sep 11, 2016

Wow, what a great response! Thanks so much!!!!
What about the 10th and 11th of October - or do we need a doodle?

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That's great for me

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Wow, what a great response! Thanks so much!!!!
What about the 10th and 11th of October - or do we need a doodle?


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leobiscassi commented Sep 11, 2016

That's great for me

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Wow, what a great response! Thanks so much!!!!
What about the 10th and 11th of October - or do we need a doodle?


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I'm on vacation from 2 to 15. October. If nothing else works, you can of course still do it without me though.

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johanneskoester commented Sep 11, 2016

I'm on vacation from 2 to 15. October. If nothing else works, you can of course still do it without me though.

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I am really looking forward to this!

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souravsingh commented Sep 18, 2016

I am really looking forward to this!

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What about the 2-3 November? Is this better?

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bgruening commented Sep 18, 2016

What about the 2-3 November? Is this better?

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Works for me!

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johanneskoester commented Sep 19, 2016

Works for me!

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Great for me too! I'm excited!

Is there an agenda? Do we all just choose things we want to contribute?

I see that there are ideas listed. I'll quite happily work on moving the perl to a perl- prefix.

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jerowe commented Sep 23, 2016

Great for me too! I'm excited!

Is there an agenda? Do we all just choose things we want to contribute?

I see that there are ideas listed. I'll quite happily work on moving the perl to a perl- prefix.

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We can use the new project board functionality that github recently integrated!

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dkoppstein commented Sep 24, 2016

We can use the new project board functionality that github recently integrated!

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@bioconda/all let's fix the data for our first online bioconda hackathon: 2-3 November! Looking forward to it!!!!

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bgruening commented Sep 24, 2016

@bioconda/all let's fix the data for our first online bioconda hackathon: 2-3 November! Looking forward to it!!!!

@bgruening bgruening changed the title from Interested in a bioconda Contribution Fest? to Bioconda Contribution Fest: 2-3 November Sep 24, 2016

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Managed to choose the exact dates of our national bioinformatics conference - but that's ok :)
http://www.abacbs.org/conference/

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tseemann commented Sep 25, 2016

Managed to choose the exact dates of our national bioinformatics conference - but that's ok :)
http://www.abacbs.org/conference/

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arg, sorry :(
Maybe you can organize a break-out session :)

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bgruening commented Sep 25, 2016

arg, sorry :(
Maybe you can organize a break-out session :)

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Another idea for the contribution fest would be to start transitioning generic packages (ex. scala) from bioconda to conda-forge, now that we're depending on the latter. It would mean we have fewer to maintain, and would also make generic packages more widely available to others.

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tomkinsc commented Sep 26, 2016

Another idea for the contribution fest would be to start transitioning generic packages (ex. scala) from bioconda to conda-forge, now that we're depending on the latter. It would mean we have fewer to maintain, and would also make generic packages more widely available to others.

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@tomkinsc please add it to the top post.

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bgruening commented Sep 26, 2016

@tomkinsc please add it to the top post.

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Any high priority issues that we should add to the backlog for this sprint?

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dkoppstein commented Sep 26, 2016

Any high priority issues that we should add to the backlog for this sprint?

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Two more ideas:

  1. Implement security enhancements (e.g. #2327)
  2. Perhaps we should set up a doodle poll for a "kickoff" google hangout of 1 hour, something like the opening session of a conference or a meet-and-greet?
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kyleabeauchamp commented Sep 26, 2016

Two more ideas:

  1. Implement security enhancements (e.g. #2327)
  2. Perhaps we should set up a doodle poll for a "kickoff" google hangout of 1 hour, something like the opening session of a conference or a meet-and-greet?
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@kyleabeauchamp added.
@dkoppstein I think everyone has a different priority list but we will introduce all our ideas and we are happy for every single contribution ... docu, code, recipes, license cleanups ....

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bgruening commented Sep 26, 2016

@kyleabeauchamp added.
@dkoppstein I think everyone has a different priority list but we will introduce all our ideas and we are happy for every single contribution ... docu, code, recipes, license cleanups ....

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For processes that can be automated, I would advocate adding functions to bioconda-utils so we can easily repeat parts of this effort in the future.

A few potential functions to automate:

  • source_url_https <package_name> — changes urls http:// -> https:// for hostnames known to support TLS (github, etc.)
  • list_sources_without_hash <package_name> [--update_recipe] — lists packages that include url: but no md5:/sha1:/sha257:/etc, perhaps with an optional argument to automatically populate hash values: download each source for a package, calculate hashes, and add to the recipe)
  • validate_recipe <package_name> — a validation function, including bioconda/bioconda-utils#19 and checks of our own: that the license field is populated, that https is used for known TLS hostnames, etc.
  • attempt_version_update <package_name> [--leave_on_build_failture] — A function to update a recipe and try to build it, where possible. For packages sourced from GitHub, this is a matter of comparing the current version with the most recent release/tag, with an optional function to convert the GitHub tag to the version used by conda (i.e. strip the preceding v from v1.x). Not sure how feasible this would be for sourceforge packages. This is in response to #2282. If the build fails after the automated update attempt, the recipe could be rolled back, or left as-is for manual fixes.

For each of these, a package name could be provided, or if omitted all bioconda packages would be used.

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tomkinsc commented Sep 29, 2016

For processes that can be automated, I would advocate adding functions to bioconda-utils so we can easily repeat parts of this effort in the future.

A few potential functions to automate:

  • source_url_https <package_name> — changes urls http:// -> https:// for hostnames known to support TLS (github, etc.)
  • list_sources_without_hash <package_name> [--update_recipe] — lists packages that include url: but no md5:/sha1:/sha257:/etc, perhaps with an optional argument to automatically populate hash values: download each source for a package, calculate hashes, and add to the recipe)
  • validate_recipe <package_name> — a validation function, including bioconda/bioconda-utils#19 and checks of our own: that the license field is populated, that https is used for known TLS hostnames, etc.
  • attempt_version_update <package_name> [--leave_on_build_failture] — A function to update a recipe and try to build it, where possible. For packages sourced from GitHub, this is a matter of comparing the current version with the most recent release/tag, with an optional function to convert the GitHub tag to the version used by conda (i.e. strip the preceding v from v1.x). Not sure how feasible this would be for sourceforge packages. This is in response to #2282. If the build fails after the automated update attempt, the recipe could be rolled back, or left as-is for manual fixes.

For each of these, a package name could be provided, or if omitted all bioconda packages would be used.

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I plan to go over all PR in the next days and label them. For example see this one: #2562

We need help from someone who owns a Mac and cares about OSX packages. If we can label PR appropriate we can use this hopefully during our hackathon.

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bgruening commented Oct 8, 2016

I plan to go over all PR in the next days and label them. For example see this one: #2562

We need help from someone who owns a Mac and cares about OSX packages. If we can label PR appropriate we can use this hopefully during our hackathon.

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I have a mac and I definitely care about OS X packages - I will participate as much as I can.

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gregvonkuster commented Oct 8, 2016

I have a mac and I definitely care about OS X packages - I will participate as much as I can.

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I have collected a few issue and tagged them as hackathon: https://github.com/bioconda/bioconda-recipes/labels/hackathon

Feel free to add more if relevant.

@gregvonkuster thanks!!!

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bgruening commented Oct 9, 2016

I have collected a few issue and tagged them as hackathon: https://github.com/bioconda/bioconda-recipes/labels/hackathon

Feel free to add more if relevant.

@gregvonkuster thanks!!!

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I'm also interested in helping with the OSX packages if I have time!
On Sun, 9 Oct 2016 at 14:52, Björn Grüning notifications@github.com wrote:

I have collected a few issue and tagged them as hackathon:
https://github.com/bioconda/bioconda-recipes/labels/hackathon

Feel free to add more if relevant.

@gregvonkuster https://github.com/gregvonkuster thanks!!!


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jrderuiter commented Oct 9, 2016

I'm also interested in helping with the OSX packages if I have time!
On Sun, 9 Oct 2016 at 14:52, Björn Grüning notifications@github.com wrote:

I have collected a few issue and tagged them as hackathon:
https://github.com/bioconda/bioconda-recipes/labels/hackathon

Feel free to add more if relevant.

@gregvonkuster https://github.com/gregvonkuster thanks!!!


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lecorguille Oct 20, 2016

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I'm in!

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lecorguille commented Oct 20, 2016

I'm in!

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vodkatad Oct 28, 2016

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Will try to join you to get a gist on how to give a hand in the future to this project.

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vodkatad commented Oct 28, 2016

Will try to join you to get a gist on how to give a hand in the future to this project.

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I updated the description a little bit and I'm starting to get exited only for days left. Please prepare a bioconda-recipes fork that is working with travis to distribute the work load a little bit. Let me know if you have any questions.

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bgruening commented Oct 29, 2016

I updated the description a little bit and I'm starting to get exited only for days left. Please prepare a bioconda-recipes fork that is working with travis to distribute the work load a little bit. Let me know if you have any questions.

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claresloggett Nov 1, 2016

I might have some blocks of time to contribute but I'm probably in a different timezone to most. What time (and timezone) are you planning to start the Hangout / Gitter?

I might have some blocks of time to contribute but I'm probably in a different timezone to most. What time (and timezone) are you planning to start the Hangout / Gitter?

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There will be a bunch of people from all over the world my hope/guess is that 24h someone will be available ... :-)

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bgruening commented Nov 1, 2016

There will be a bunch of people from all over the world my hope/guess is that 24h someone will be available ... :-)

@bgruening bgruening referenced this issue Nov 1, 2016

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Exparna #2673

2 of 4 tasks complete
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@bioconda/all just a few our and we will start our first bioconda hackathon. Please prepare yourself with our PreHack list:

PreHack preparation:

Moreover, we have tagged Issues that seems to be suitable for a Hackathon, please see:
https://github.com/bioconda/bioconda-recipes/labels/hackathon

See you all on gitter: https://gitter.im/bioconda/Lobby

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bgruening commented Nov 1, 2016

@bioconda/all just a few our and we will start our first bioconda hackathon. Please prepare yourself with our PreHack list:

PreHack preparation:

Moreover, we have tagged Issues that seems to be suitable for a Hackathon, please see:
https://github.com/bioconda/bioconda-recipes/labels/hackathon

See you all on gitter: https://gitter.im/bioconda/Lobby

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claresloggett Nov 1, 2016

Ah sorry, my feed had not updated with the Gitter link. I see it now!

claresloggett commented Nov 1, 2016

Ah sorry, my feed had not updated with the Gitter link. I see it now!

@bgruening bgruening closed this Jul 27, 2017

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