,

On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hi Peter,
>
> On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster <g...@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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to