,

On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
> Hi Peter,
>
> On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
>>>

>>> In any case, we have a fix for out move_directory_files which
>>> Dave is now committing.  So your tests should pass with tonight's
>>> run - Let's hope!
>>

>> That explanation makes perfect sense to me - but I can
>> see it took some digging to solve it!
>>
>> There is actually one MIRA binary (mira) and several aliases
>> (e.g. mirabait) which are really symlinks back to mira. Magic.

For anyone interested, the fix was this commit:
https://bitbucket.org/galaxy/galaxy-central/commits/a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21

>> My next query would be: why wasn't the failing action
>> <move_directory_files> being caught as a failed install?

Scanning over the code, some of the actions have explicit error
handling but make_directory, move_directory_files, move_file
and others do not. I guess any exception is propagated up...
lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py

> 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!

> Here is the entire log of the installtion process that helped us uncover the
> problem - notice that upon failure of the initial binary installation, the
> process "proceeds with install and compile recipe for tool dependency MIRA".

Would it be a security risk to automatically expose these logs?

Peter
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