Hello Peter,

On Feb 20, 2014, at 10:20 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> 
>> On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock <p.j.a.c...@googlemail.com> 
>> wrote:
>>> On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>>>> Your installation recipe for mira attempts to download a binary and if that
>>>> fails, it echoes an error, but still performs <set_environment> actions..
>>> 
>>> Ah - I can see that now, I need a fall back <action> tag which
>>> either tries to compile MIRA or raises an explicit error. Thanks!
>> 
>> Sorry, slightly confused: there was a fallback <action> tag which
>> was and is meant to raise an error. It was accidentally raising an
>> error due to a bash syntax error in my unquoted echo (which that
>> detailed log you posted alerted me to), now fixed in my repository
>> and uploaded to the Test Tool Shed:
>> https://github.com/peterjc/pico_galaxy/commit/4b003cf9b5e6baa15c75bb65723c5af78e40c18d
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>> 
>> The BLAST+ packages have the same glitch in their fall-back
>> (so I will need to update them on the main and test Tool Shed,
>> although I will delay that pending your reply to the problem below):
>> https://github.com/peterjc/galaxy_blast/commit/4b2fa1fbf485c4630cb6dc0beaf7286cb103bd71
>> 
>> So, what happens is first the arch/os specific actions is tried, here
>> <actions os="linux" architecture="x86_64">
>> 
>> That was failing with MIRA4 due to the symlink bug (now fixed).
>> Because the platform specific action failed, the generic <actions>
>> was used - where I deliberately try to raise an error to signal
>> the installation failed.
>> 
>> What is surprising me is that the Tool Shed see the error, logs
>> it, but still continues on (setting my environment variables, and
>> reporting success). Why is that?
> 
> I'll need some time to investigate this behavior - if I discover a framework 
> issue, I'll provide a fix.

The above issue should be corrected in 
https://bitbucket.org/galaxy/galaxy-central/commits/f5a119ac52a957204ab968a78638fe2a942c6893
 which is currently running on the Test Tool Shed.  I'm going to wait for 
tonight's Install and Test run on the Test Tool Shed to make sure all is well 
with the fix.  If things look good we'll graft the fix to the stable branch 
tomorrow.  Thanks for reporting this!

As we briefly discussed earlier, your mira4 recipe is not currently following 
best practices.  Although you uncovered a problem in the framework which has 
now been corrected, your recipe's fall back <actions> tag set should be the 
recipe for installing mira4 from source ( 
http://sourceforge.net/projects/mira-assembler/ ) since there is no licensing 
issues for doing so.  This would be a more ideal approach than echoing the 
error messages.

Thanks very much for helping us discover this problem though!

Greg Von Kuster

> 
>> 
>> Thanks,
>> 
>> Peter
>> 
>> P.S. The assert file exists action I suggested previously would
>> be a neat way to catch some failing installs, e.g. here I
>> expected the executables $MIRA4/mira and $MIRA4/mirabait
>> etc to exist. I've filed a Trello card for this enhancement idea:
>> 
>> https://trello.com/c/xBUhFvj0/1446-add-assert-file-exists-and-directory-exists-actions-to-tool-dependencies-xml
> 
> Thanks - I've moved it to the Tool Shed Trello Board - its in Project in 
> Planning.
> 
> Greg Von Kuster
> 
> 
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> 
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