Ok, thanks for all the quick feedback folks, and your tool links John.  So much 
work rolling off everyone's presses!

John, on <command> and nixing interpreter="" : Ok, I like that, to change it so 
that people can see <command> tag is a place for shell interaction. 

Re. Update / Revision distinction:
So looking at this in detail (Peter and Martin ;) ) - it turns out the "update" 
and "revision" terms are actually from "Install latest revision" vs "Get 
updates" options that occur in the Galaxy interface (you can see from snapshots 
I did of galaxy admin view in tool versioning tutorial) when downloading tool 
updates.  So my definitions were an attempt to explain the difference there.
Perhaps then we should have a ticket to have Galaxy force any toolshed update 
to have a version id that increments, then no opportunity for confusion, and no 
need for "update" phrase in galaxy UI? 

In tutorial I do want to show people the implications of not incrementing. ... 
I'll let trainees know that incrementing a tool version number leads to a 
separately selectable tool version to run.  To keep an up-to-date Galaxy 
install is to engage the admin to be bringing in these tool versions/choices 
more frequently even though they functionally don't do anything different.  
Advice is to encourage the dev to batch their changes into just a few revisions 
per year say for main Galaxy toolshed.  I've downgraded this whole "update" 
thing to just say its possible to upload a change without version increment but 
not advisable for main toolshed.  



P.s. for the ffp_phylogeny tool I wanted to do piping in the <command> tag  
e.g. "<command>progx -a | progy -b -c | progz</command>".  Easy enough unless 
one wants to catch errors when they happen within the piped processes.  I found 
that verbatim one would unfortunately never see any error info from earlier 
stages of the pipe on return to Galaxy, right?.  I took a stab at writing a 
"check_output(command)" call in ffp_phylogeny tool that sets up error reporting 
for each stage of pipe, which seems to do ok (though only tested manually), but 
wondering if anyone else has tackled the piping error reporting?

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
From: John Chilton [jmchil...@gmail.com]
Sent: Friday, March 13, 2015 7:56 AM
To: Peter Cock
Cc: Martin Čech; galaxy-...@lists.bx.psu.edu; Hsiao, William; Dooley, Damion
Subject: Re: [galaxy-dev] Comment on Training Documentation

Awesome work Damion - thanks for publishing and sharing these! I hope
the workshop goes well.

I recently created a wiki page just with tool development resource links


that now gets embedded in other more common landing pages including


I have added links to your content from to this resource list.

One quick thought on the content. The interpreter="python" idiom for
wrappers has been around for years and is used widely but it has some
serious drawbacks - in particular nothing can come before the wrapper
in the tool XML - no cheetah directives like #import or #set and no
linking in files (for instance the following setup idiom:

ln -s "${input_bam}" temp_input.bam &&
ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai &&
actual_command --args

In the planemo documentation I am not going to mention interpreter for
this reason - I think it is frustrating for people when it does not
work the way intuitively it should. The forthcoming 15.03 injects a
new variable called $__tool_directory__ that I think should be the new
best practice.

ln -s "${input_bam}" temp_input.bam &&
ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai &&
python $__tool_directory__/wrapper.py --args

I understand that it might be best to not base your tutorial on
features not even released yet :) - but I did want to take the
opportunity to mention this idiom.

As you mentioned I have also been working on updated tool development
documentation lately at (http://planemo.readthedocs.org/en/latest/). I
am trying to build a set of smaller resources that can be composed
into tailored resources (e.g. build tools without planemo, with
planemo, with planemo virtual appliance), (normal tutorial, verbose
tutorial, slide-based tutorial), (with and without Docker). I don't
know if rst is up to this task, but we will see.

Another effort along these lines worth checking out is Kyle's tool
tutorial - https://github.com/kellrott/galaxy-tooldev-docs/tree/master/docs.
This tutorial is focused on using the planemo appliance and
Dockerizing tools.


On Fri, Mar 13, 2015 at 4:35 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Fri, Mar 13, 2015 at 12:23 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>> Your tutorial looks great Damion! Thank you for sharing.
>> I am not sure about the vocabulary you are trying to estabilish though
>> (update vs revision). I understand what you mean but I would just stick with
>> 'If the tool changed behavior you have to bump the version.' No need to
>> specifically name the steps as it can cause confusion (revision has a
>> different meaning in version control world).
> I was also confused about your (Damion's) update vs revision terminology,
> and agree with Martin that any behaviour change (especially bug fixes,
> even minor ones) should come with a version change.
> I've not had time to look at your slides, but thanks for sharing them.
> Peter
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