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IUC Tools & Collections Hackathon (Fall 2015) #239

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jmchilton opened this Issue Aug 4, 2015 · 41 comments

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jmchilton commented Aug 4, 2015

We are planning a remote hackathon on September 17th and 18th for Galaxy tool developers to work mainly on dataset collections.

Dataset collections enable MapReduce style workflows in Galaxy and have come a long way over the last year+. Several groups are using dataset collections and newer tools to express workflows of various degrees of complexity that were not possible in Galaxy before.

The remote nature of this gives people who don't have the opportunity to come to GCC hackathons (which have always been productive and a lot of fun) a chance to participate in a Galaxy hackathon. Having a well defined topic will allow us to accomplish a lot and let people who don't have particular tasks in mind find something to work on very quickly.

We are collecting ideas to work on, but we expect to attract the most participation by simply getting tool developers interested in getting help adding collection support to their existing tools and workflows to show up and participate.

If you are interested in participating in the hackathon but not interested in actual tool development - we will assemble a list of smaller, manageable Python and JavaScript tasks to work on and certainly documentation is a chronically lacking for collections so we could use help there and no actual coding would be required.

This is the first remote hackathon we have organized and we encourage ideas or advice about how to organize it please let us know. A core group of will be available on IRC all day and we will have 4 google
hangouts across those days to organize, answer questions, and report progress.

We will do our best to coordinate and make this hackathon a nice and productive experience and we would like to especially focus on working reasonable hours and discourage overnighters.

All forms of contribution are welcome!

Original idea from @bgruening (galaxyproject/tools-devteam#26 (comment)).

Tools to update:

Just ideas if these don't make sense remove them

New Tools:

  • Tabular tools (some of this may be covered by unix tools)
    • concatenate rows together and add columns for collection identifiers
    • concatenate columns to a table for each element in a collection (ever a use for this?)
    • Split out a table based on unique values in column (1 table -> collection of tables) split_file_on_column.xml
  • Tool for concatenating plain textual data (ignoring identifiers I guess)
  • Create a tool that takes in a bam file and produces collection of regions (bed files).
    • Document a simple workflow that uses this to parallelize work over a bam file in a workflow.
  • Ensure we have sufficient coverage to merge/reduce various other formats.
    • bam/sam
    • ...

general updates

  • Replace <repeats> where needed with multiple="True" in
    • tools-iuc
    • tools-devteam
    • galaxytools
  • migrate the text manipulation tools (unix-tools) to perform reduce steps

Documentation:

  • Update planemo collection documentation to include information on creating tools that output collections. Add planemo docs for BB PR #634 and Git PR #538.
  • Document using regions to parallelize work over a bam file in a workflow as a tip in planemo docs.
  • Document using read group macros and general techniques for dealing with read groups in a collection aware fashion in planemo docs. Potentially based off tools-devteam #103.
  • Add visual descriptions of various map & reduce operations to planemo documentation.
  • Add end user documentation for using collections in tools. Histories has nice documentation here, but I don't think similar documentation exists for tools.

@jmchilton jmchilton changed the title from Summer 2015 Tools and Collection Hackathon to Summer 2015 Tools and Collections Hackathon Aug 4, 2015

@jmchilton jmchilton changed the title from Summer 2015 Tools and Collections Hackathon to Summer 2015 Tools & Collections Hackathon Aug 4, 2015

@jmchilton jmchilton changed the title from Summer 2015 Tools & Collections Hackathon to IUC Tools & Collections Hackathon (Summer 2015) Aug 4, 2015

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I made a few updates, thanks John for putting this together.
@jj-umn @iracooke Do you have time to join and work on proteomic tools?

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bgruening commented Aug 4, 2015

I made a few updates, thanks John for putting this together.
@jj-umn @iracooke Do you have time to join and work on proteomic tools?

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👍 thanks for creating an issue to track this :)

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erasche commented Aug 4, 2015

👍 thanks for creating an issue to track this :)

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Going to send out an announcement to galaxy-dev to drum up support - anyone want to review before I send? I am signing it as IUC so someone from the IUC should probably actually review it :). https://docs.google.com/document/d/1vXkITrzmZTDWFMDe8__JoqdaK6YBUXxqpbzglapEcqw/edit?usp=sharing

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jmchilton commented Aug 10, 2015

Going to send out an announcement to galaxy-dev to drum up support - anyone want to review before I send? I am signing it as IUC so someone from the IUC should probably actually review it :). https://docs.google.com/document/d/1vXkITrzmZTDWFMDe8__JoqdaK6YBUXxqpbzglapEcqw/edit?usp=sharing

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@jmchilton awesome! So excited! :)

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erasche commented Aug 10, 2015

@jmchilton awesome! So excited! :)

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@jmchilton I'm in on this too! Should be fun.

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nturaga commented Aug 10, 2015

@jmchilton I'm in on this too! Should be fun.

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Perfect! Please send it as it is :)

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bgruening commented Aug 10, 2015

Perfect! Please send it as it is :)

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I am in, obviously.

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martenson commented Aug 10, 2015

I am in, obviously.

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I'm in!

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mr-c commented Aug 11, 2015

I'm in!

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Can this be a contribution fest instead of a hackathon? I enjoyed Mozilla Science Lab's emphasis on only working what would be ones normal hours, no all nighters..

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mr-c commented Aug 11, 2015

Can this be a contribution fest instead of a hackathon? I enjoyed Mozilla Science Lab's emphasis on only working what would be ones normal hours, no all nighters..

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+1 for wording. Most of us already work crazy enough hours and this is to
be friendly/happy/fun collections dev event.

tir. 11. aug. 2015 kl. 18.11 skrev Michael R. Crusoe <
notifications@github.com>:

Can this be a contribution fest instead of a hackathon? I enjoyed Mozilla
Science Lab's emphasis on only working what would be ones normal hours, no
all nighters..


Reply to this email directly or view it on GitHub
#239 (comment)
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erasche commented Aug 12, 2015

+1 for wording. Most of us already work crazy enough hours and this is to
be friendly/happy/fun collections dev event.

tir. 11. aug. 2015 kl. 18.11 skrev Michael R. Crusoe <
notifications@github.com>:

Can this be a contribution fest instead of a hackathon? I enjoyed Mozilla
Science Lab's emphasis on only working what would be ones normal hours, no
all nighters..


Reply to this email directly or view it on GitHub
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Hmm... I have lobbied repeatedly internally to change the hackathon wording for the GCC events. I think a reason to keep the unfortunate hackathon name for this event is to establish some sort of lineage or branding shared between the GCC events and these ones - so I am + .5 on this change.

@bgruening you first termed this a hackathon (galaxyproject/tools-devteam#26 (comment)), any thoughts on change the name?

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jmchilton commented Aug 12, 2015

Hmm... I have lobbied repeatedly internally to change the hackathon wording for the GCC events. I think a reason to keep the unfortunate hackathon name for this event is to establish some sort of lineage or branding shared between the GCC events and these ones - so I am + .5 on this change.

@bgruening you first termed this a hackathon (galaxyproject/tools-devteam#26 (comment)), any thoughts on change the name?

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I guess this is more a cultural thing. For me the word hackathon is associated with a lot of fun, productive work and a nice atmosphere. I would never expect that someone feels urged to participate (after or in normal working hours). People are free to choose and we do not emphasize anything here, at least this was not my attention. It's all about fun, learning and contributing to a project we all love.
But maybe I'm just too naive here :)

I'm fine with the change if you think it's more appropriate. Codefest is the other possibility from BOSC.

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bgruening commented Aug 12, 2015

I guess this is more a cultural thing. For me the word hackathon is associated with a lot of fun, productive work and a nice atmosphere. I would never expect that someone feels urged to participate (after or in normal working hours). People are free to choose and we do not emphasize anything here, at least this was not my attention. It's all about fun, learning and contributing to a project we all love.
But maybe I'm just too naive here :)

I'm fine with the change if you think it's more appropriate. Codefest is the other possibility from BOSC.

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I have lots of positive association with the GCC events I've been at. Alas
in the Bay area it has a quite different connotation. Easy compromise would
be to keep the name but be explicit in the description.

On Wed, Aug 12, 2015 at 6:27 AM Björn Grüning notifications@github.com
wrote:

I guess this is more a cultural thing. For me the word hackathon is
associated with a lot of fun, productive work and a nice atmosphere. I
would never expect that someone feels urged to participate (after or in
normal working hours). People are free to choose and we do not emphasize
anything here, at least this was not my attention. It's all about fun,
learning and contributing to a project we all love.
But maybe I'm just too naive here :)

I'm fine with the change if you think it's more appropriate. Codefest is
the other possibility from BOSC.


Reply to this email directly or view it on GitHub
#239 (comment)
.

Michael R. Crusoe: Programmer & Bioinformatician crusoe@ucdavis.edu
The lab for Data Intensive Biology; University of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

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mr-c commented Aug 12, 2015

I have lots of positive association with the GCC events I've been at. Alas
in the Bay area it has a quite different connotation. Easy compromise would
be to keep the name but be explicit in the description.

On Wed, Aug 12, 2015 at 6:27 AM Björn Grüning notifications@github.com
wrote:

I guess this is more a cultural thing. For me the word hackathon is
associated with a lot of fun, productive work and a nice atmosphere. I
would never expect that someone feels urged to participate (after or in
normal working hours). People are free to choose and we do not emphasize
anything here, at least this was not my attention. It's all about fun,
learning and contributing to a project we all love.
But maybe I'm just too naive here :)

I'm fine with the change if you think it's more appropriate. Codefest is
the other possibility from BOSC.


Reply to this email directly or view it on GitHub
#239 (comment)
.

Michael R. Crusoe: Programmer & Bioinformatician crusoe@ucdavis.edu
The lab for Data Intensive Biology; University of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

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This sounds like a lot of fun, and I'm sure we can gather a (small) group to work on this at SANBI. I'm currently busy surveying our NGS workflows to see how they intersect the list.

I prefer the term codefest to hackathon btw.

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pvanheus commented Aug 27, 2015

This sounds like a lot of fun, and I'm sure we can gather a (small) group to work on this at SANBI. I'm currently busy surveying our NGS workflows to see how they intersect the list.

I prefer the term codefest to hackathon btw.

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We can call it keyboard-typing-time-together. :)

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martenson commented Aug 27, 2015

We can call it keyboard-typing-time-together. :)

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Has a date been picked?

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mr-c commented Aug 30, 2015

Has a date been picked?

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tnabtaf Aug 31, 2015

+1 on what Michael just said.

tnabtaf commented Aug 31, 2015

+1 on what Michael just said.

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Sure, let's go with the tenative dates, I wanted to get the Canadians involved but they are busy all month. I'm out for a while, anyone willing to update the description here and add some language about working reasonable hours?

I say we call this one a hackathon, but I'll be sure to continue the discussion.

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jmchilton commented Sep 1, 2015

Sure, let's go with the tenative dates, I wanted to get the Canadians involved but they are busy all month. I'm out for a while, anyone willing to update the description here and add some language about working reasonable hours?

I say we call this one a hackathon, but I'll be sure to continue the discussion.

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@jmchilton I modified the first post with information from emails and some words about reasonable hours.
We should coordinate timezones next.

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martenson commented Sep 1, 2015

@jmchilton I modified the first post with information from emails and some words about reasonable hours.
We should coordinate timezones next.

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boratonAJ Sep 2, 2015

Ok, I'm in.

boratonAJ commented Sep 2, 2015

Ok, I'm in.

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Sounds great, it's on my calendar.

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lparsons commented Sep 3, 2015

Sounds great, it's on my calendar.

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@tnabtaf could we get this on the calendar please?

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erasche commented Sep 3, 2015

@tnabtaf could we get this on the calendar please?

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@martenson any ideas how to coordinate this? I will be online from 9.00-21.00+ and will try to help wherever I can. Can we use #galaxyproject in freenode or should we use a separate channel?

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bgruening commented Sep 7, 2015

@martenson any ideas how to coordinate this? I will be online from 9.00-21.00+ and will try to help wherever I can. Can we use #galaxyproject in freenode or should we use a separate channel?

@jmchilton jmchilton changed the title from IUC Tools & Collections Hackathon (Summer 2015) to IUC Tools & Collections Hackathon (Fall 2015) Sep 16, 2015

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dannon commented Sep 16, 2015

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10 AM Eastern Standard Time (UTC−05:00) or Eastern Daylight Time
(UTC−05:00) ?

I think you mean the latter :-)

See y'all tomorrow!

In the past I've been encouraged to send a link to a timezone website like
http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150917&p1=179&p2=3736

On Wed, Sep 16, 2015 at 2:08 PM Dannon Baker notifications@github.com
wrote:

Hangout for tomorrow@10AM EST
https://plus.google.com/u/0/events/cnjf2mqg7vl6aigs5fkai6dh4rk


Reply to this email directly or view it on GitHub
#239 (comment)
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mr-c commented Sep 16, 2015

10 AM Eastern Standard Time (UTC−05:00) or Eastern Daylight Time
(UTC−05:00) ?

I think you mean the latter :-)

See y'all tomorrow!

In the past I've been encouraged to send a link to a timezone website like
http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150917&p1=179&p2=3736

On Wed, Sep 16, 2015 at 2:08 PM Dannon Baker notifications@github.com
wrote:

Hangout for tomorrow@10AM EST
https://plus.google.com/u/0/events/cnjf2mqg7vl6aigs5fkai6dh4rk


Reply to this email directly or view it on GitHub
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Yep, I'd already updated it -- gotta read github comments on github and not email, since there's no notification of edits! (something I've requested from GitHub numerous times)

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dannon commented Sep 16, 2015

Yep, I'd already updated it -- gotta read github comments on github and not email, since there's no notification of edits! (something I've requested from GitHub numerous times)

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Hello everyone!
Today and tomorrow we will try to improve Galaxy tools to consume and create collections.
You are welcome to join and contribute in any way. For example code contributions, not matter how small, but also in improving documentations and our best-practice guide.

If you have any questions, suggestions, bugs .... please get in touch with us on:

I would also like to start a proper documentation about collections and collect tips in this document with the aim to move parts of it back into the tool documentation as well as the best-practice guide.

Have a lot of fun!
Bjoern

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bgruening commented Sep 17, 2015

Hello everyone!
Today and tomorrow we will try to improve Galaxy tools to consume and create collections.
You are welcome to join and contribute in any way. For example code contributions, not matter how small, but also in improving documentations and our best-practice guide.

If you have any questions, suggestions, bugs .... please get in touch with us on:

I would also like to start a proper documentation about collections and collect tips in this document with the aim to move parts of it back into the tool documentation as well as the best-practice guide.

Have a lot of fun!
Bjoern

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ghost Sep 17, 2015

Just a note that now I'm doing a quality control tool that touches on the extraction of log/job status data from workflow log files, for reporting and to trigger stop/error states. Runs off of a list of rules (predefined text-mining functions like regex etc. applied to specific log files to create temp variables and final report outputs in json format). May be of interest to others?

ghost commented Sep 17, 2015

Just a note that now I'm doing a quality control tool that touches on the extraction of log/job status data from workflow log files, for reporting and to trigger stop/error states. Runs off of a list of rules (predefined text-mining functions like regex etc. applied to specific log files to create temp variables and final report outputs in json format). May be of interest to others?

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@Public-Health-Bioinformatics sounds interesting, but I don't think I fully understand it :)

Coders: The second trimmer is updated and ready for a review: bgruening/galaxytools#245

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bgruening commented Sep 17, 2015

@Public-Health-Bioinformatics sounds interesting, but I don't think I fully understand it :)

Coders: The second trimmer is updated and ready for a review: bgruening/galaxytools#245

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@Public-Health-Bioinformatics might be useful in the (recently added) advanced exit code detection routines in galaxy. Can link information tomorrow.

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erasche commented Sep 18, 2015

@Public-Health-Bioinformatics might be useful in the (recently added) advanced exit code detection routines in galaxy. Can link information tomorrow.

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The second day of our Codefest has begun. Anyone wants to work on the new tools? It should be possible to implement them with standard unix tools and a little bit of collection magic! :)

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bgruening commented Sep 18, 2015

The second day of our Codefest has begun. Anyone wants to work on the new tools? It should be possible to implement them with standard unix tools and a little bit of collection magic! :)

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I'll claim swapping out repeats with multiple="True".

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erasche commented Sep 18, 2015

I'll claim swapping out repeats with multiple="True".

erasche added a commit that referenced this issue Sep 18, 2015

erasche added a commit to galaxyproject/tools-devteam that referenced this issue Sep 18, 2015

erasche added a commit to bgruening/galaxytools that referenced this issue Sep 18, 2015

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@jmchilton is this suiteable to check off the "Tool for concatenating plain textual data (ignoring identifiers I guess)" item?
https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/text_processing/cat.xml

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bgruening commented Sep 18, 2015

@jmchilton is this suiteable to check off the "Tool for concatenating plain textual data (ignoring identifiers I guess)" item?
https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/text_processing/cat.xml

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This is the PR for the work we did at SANBI-SA: galaxyproject/tools-devteam#227 and blog with a little documentation http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collections/

@Public-Health-Bioinformatics sounds interesting, Jen specifically mentioned at GCC 2015 that she'd like to be able to decide whether a workflow can continue or should abort based on quality control, perhaps your work feeds into this goal.

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pvanheus commented Sep 19, 2015

This is the PR for the work we did at SANBI-SA: galaxyproject/tools-devteam#227 and blog with a little documentation http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collections/

@Public-Health-Bioinformatics sounds interesting, Jen specifically mentioned at GCC 2015 that she'd like to be able to decide whether a workflow can continue or should abort based on quality control, perhaps your work feeds into this goal.

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And now... what next? Is there a wrap-up for the codefest planned? If so, who is writing it? And when's the next one?

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pvanheus commented Sep 20, 2015

And now... what next? Is there a wrap-up for the codefest planned? If so, who is writing it? And when's the next one?

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@jmchilton is this suiteable to check off the "Tool for concatenating plain textual data (ignoring identifiers I guess)" item?
https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/text_processing/cat.xml

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bgruening commented Sep 21, 2015

@jmchilton is this suiteable to check off the "Tool for concatenating plain textual data (ignoring identifiers I guess)" item?
https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/text_processing/cat.xml

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@pvanheus I will try to collect all PR and write a small summary here. If I can get more time to devote to this I will try to do this kind of events more regularly. Maybe every two month?

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bgruening commented Sep 21, 2015

@pvanheus I will try to collect all PR and write a small summary here. If I can get more time to devote to this I will try to do this kind of events more regularly. Maybe every two month?

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ghost Sep 25, 2015

@erasche You mentioned "advanced exit code detection routines in galaxy." I would like more info on that. My QC tool basically lets one set up rules that trigger whether to stop a job or continue, as well as reporting on QC metrics. I'm now at the point where I need to code the stop a job part. Assuming its just a matter of exit code 1, but if you folks have some new options or things to understand I'd like to learn.

Thanks,

Damion

ghost commented Sep 25, 2015

@erasche You mentioned "advanced exit code detection routines in galaxy." I would like more info on that. My QC tool basically lets one set up rules that trigger whether to stop a job or continue, as well as reporting on QC metrics. I'm now at the point where I need to code the stop a job part. Assuming its just a matter of exit code 1, but if you folks have some new options or things to understand I'd like to learn.

Thanks,

Damion

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@Public-Health-Bioinformatics sorry, I knew there was someone I was supposed to forward documentation to, my apologies. galaxyproject/galaxy#117 implemented functionality that provided an easier alternative to the exit code detection stuff. You simply add the detect_errors="..." to your <command/> block, like in this example and that replaces doing it the old way with regex

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erasche commented Sep 25, 2015

@Public-Health-Bioinformatics sorry, I knew there was someone I was supposed to forward documentation to, my apologies. galaxyproject/galaxy#117 implemented functionality that provided an easier alternative to the exit code detection stuff. You simply add the detect_errors="..." to your <command/> block, like in this example and that replaces doing it the old way with regex

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