if a tool failed we all really benefit from seeing as much as we can - as securely as we can. Can we safely expose them somewhere protected?
On Thu, Feb 20, 2014 at 8:59 PM, 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: > > 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/ >
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