Hi,
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.
Cheers,
Damion
P.s. for the ffp_phylogeny tool I wanted to do piping in the command tag
e.g. commandprogx -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
https://wiki.galaxyproject.org/Develop/ResourcesTools
that now gets embedded in other more common landing pages including
https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
https://wiki.galaxyproject.org/Develop
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.
-John
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
