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?

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
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