Re: [galaxy-dev] Best way to work with one directory and many files as 1 input
by Pierre Pericard
Hi Christos,
Yes, I would be very interested by your modified file.
I'm forwarding to the mailing-list so this bug can be listed.
Thanks,
Pierre
Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS - UPMC
Place Georges Teissier
CS 90074
29688 ROSCOFF CEDEX
FRANCE
Tel : (+33) 2 98 29 56 46
http://abims.sb-roscoff.fr/
Le 01/02/2013 00:34, chriskannas(a)gmail.com a écrit :
> Hi,
>
> I'm working on the same thing, having a composite dataset with many files in many sub-folders.
>
> Well during the development & testing of the tool that uses this composite datatype, I found out that Galaxy does not handle correctly sub-dirs, it works pretty good with files but if it finds a sub-dir then the copy messes it up.
>
> To be more specific it uses shutil.copy without checking if it is file or directory, when coping dirs it has to use shutil.copytree.
>
> I managed to make our local Galaxy installation to handle them quite ok with some modifications in method DiskObjectStor.update_from_file(...) located in lib/galaxy/objectstore/__init__.py
>
> I can send you a copy of the file I've modified.
>
> Regards,
> Christos
>
> ------
>
> Christos Kannas
> Researcher
> Ph.D Student
>
> e-Health Laboratory
> Dept. Computer Science,
> University of Cyprus
>
> <quote author='Pierre Pericard'>
> Ok, thanks a lot, I'll try and get back to the mailing list if other
> problems seem to occur.
>
> Pierre.
>
>
> Pierre Pericard
> IE CDD - Projet Peptisan
>
> Service Informatique et Bio-informatique (SIB)
> Station Biologique de Roscoff
> CNRS-UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff CEDEX
> FRANCE
> http://abims.sb-roscoff.fr/
>
> Le 30/01/2013 11:45, Ross a écrit :
>> I'd suggest:
>> 1) Make your new datatype a subclass of Html - it's a subclass of
>> composite that contains an HTML document as the object's native
>> display - so it can inform users what's there.
>>
>> 2) When constructing these new things, pass the file_path of the Html
>> (composite) dataset subclass to your wrapper on the command line
>>
>> 3) Your wrapper code can construct any arbitrary structure as long as
>> it's rooted in that directory - Galaxy stores it without any fuss. The
>> wrapper should also populate the Html file itself with nicely
>> laid annotation for the user to check out.
>>
>> 4) The key is that all tools that take this new datatype as input must
>> know how to decode this structure - they must be passed the
>> $input.extra_files_path which gives them that same path root.
>>
>> 5) Yes, it's odd and annoying that it's extra_files_path for
>> files_path. Go figure.
>>
>> 6) grep extra_files tools/*.xml to find some examples - I think the
>> velvetg one uses a complex subdirectory structure - but it doesn't
>> really matter - as long as your tools know how to deal with it, it's
>> just a directory to Galaxy!
>> I hope all this helps...
>>
>>
>> On Wed, Jan 30, 2013 at 8:22 PM, Pierre Pericard
>> <pierre.pericard(a)sb-roscoff.fr <mailto:pierre.pericard@sb-roscoff.fr>>
>> wrote:
>>
>> In that case, could anyone point me to an example of a Composite
>> Datatype which could accept as input an unknown number of files in
>> an unknown number of directories. I can't seem to understand how
>> that would work based on the wiki.
>>
>> But maybe are we anticipating a near functionality of Galaxy.
>> There were talks about changing the way Galaxy handle zip files,
>> is it still on the table ?
>>
>> Thank in advance for any help,
>>
>> Pierre
>>
>>
>>
>> Pierre Pericard
>> IE CDD - Projet Peptisan
>>
>> Service Informatique et Bio-informatique (SIB)
>> Station Biologique de Roscoff
>> CNRS-UPMC
>> Place Georges Teissier
>> CS 90074
>> 29688 Roscoff CEDEX
>> FRANCE
>> http://abims.sb-roscoff.fr/
>>
>> Le 29/01/2013 18:04, Peter Cock a écrit :
>>
>> On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard
>> <pierre.pericard(a)sb-roscoff.fr
>> <mailto:pierre.pericard@sb-roscoff.fr>> wrote:
>>
>> If I'm not mistaking, Composite Datatypes allow for only
>> one directory,
>> whereas we need to keep a constant directory structure
>> with 2 or more
>> sub-directories containing our input files.
>>
>> I'm not sure if that is true - the example of HTML output with
>> images
>> comes to mind as a common use-case where subfolder(s) would be
>> expected. I've only had limited first hand experience with
>> Galaxy's
>> composite datatypes myself though.
>>
>> We have no way to change these tools behavior (obviously
>> not Galaxy-friendly
>> ;-) ) and therefore need to maintain this structure in the
>> job working
>> directory.
>>
>> Perhaps a tool wrapper could create a dummy folder using symlinks
>> (faster and less wasted disk than copying files), but that
>> isn't ideal.
>>
>> Peter
>>
>>
>> ___________________________________________________________
>>
>
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> </quote>
> Quoted from:
> http://dev.list.galaxyproject.org/Best-way-to-work-with-one-directory-and...
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Cardinale Stefano
Postdoctoral researcher
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Department of Bioengineering
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