A brief writeup of my experiences:
http://web.science.mq.edu.au/~cassidy/wordpress/2015/10/21/galaxy-tool-generating-datasets/
Steve
On 21 October 2015 at 18:27, Peter van Heusden <p...@sanbi.ac.za> wrote:
> These names have meaning in CollectedDatasetMatch:
>
> designation means designation if that exists else name
> name means name
> dbkey means dbkey
> ext means ext
> visible means visible
>
>
> On 21 October 2015 at 08:44, Steve Cassidy <steve.cass...@mq.edu.au>
> wrote:
>
>> Thanks, yes that works, though I'm not really sure what the difference is
>> between __name__ and __designation__. They both seem to have the same
>> effect in my example.
>>
>> Thanks for your help.
>>
>> Steve
>>
>>
>> On 21 October 2015 at 16:49, Peter van Heusden <p...@sanbi.ac.za> wrote:
>>
>>> Since you're using a directory, you can use one of the built in patterns:
>>>
>>> DEFAULT_EXTRA_FILENAME_PATTERN =
>>> r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
>>>
>>> NAMED_PATTERNS = {
>>> "__default__": DEFAULT_EXTRA_FILENAME_PATTERN,
>>> "__name__": r"(?P<name>.*)",
>>> "__designation__": r"(?P<designation>.*)",
>>> "__name_and_ext__": r"(?P<name>.*)\.(?P<ext>[^\.]+)?",
>>> "__designation_and_ext__": r"(?P<designation>.*)\.(?P<ext>[^\._]+)?",
>>> }
>>>
>>> In terms of docs, I don't know what the future is - the Galaxy wiki or
>>> http://galaxy.readthedocs.org/en/master/
>>>
>>>
>>> On 21 October 2015 at 04:26, Steve Cassidy <steve.cass...@mq.edu.au>
>>> wrote:
>>>
>>>> Ah, thankyou, yes, I can now get results by using patterns to match the
>>>> output. I used your example but prepend 'simple' to the filename and then
>>>> searches for that with:
>>>>
>>>> <discover_datasets pattern="simple(?P<name>.*)" />
>>>> this solves the problem for the sample script but not generally since
>>>> in general I can't predict the filenames that will be generated - this is a
>>>> tool for downloading data from a repository which could be text, audio or
>>>> video data.
>>>>
>>>> If I don't use the 'simple' prefix and omit the file extension I still
>>>> get my data but I also get three other files which are temporary scripts
>>>> generated by galaxy and placed in the working directory. So, back to
>>>> trying to put things in a subdirectory. It turns out that the issue I was
>>>> having was as you pointed out earlier, the directory attribute to
>>>> discover_datasets doesn't allow variables, so I need to write to a fixed
>>>> directory name:
>>>>
>>>> <discover_datasets pattern="(?P<name>.*)" directory="
>>>> SampleDataset" />
>>>> This now works!
>>>>
>>>> I had thought that I'd need to use a unique directory name but since
>>>> galaxy runs each job in a separate directory, this isn't required. My real
>>>> tool now works too after following the same pattern.
>>>>
>>>> Thanks for your help. I'll see if I can write this up in a blog post.
>>>>
>>>> Steve
>>>>
>>>>
>>>>
>>>> On 21 October 2015 at 00:06, Peter van Heusden <p...@sanbi.ac.za> wrote:
>>>>
>>>>> I poked around at your tool XML and the code a bit and the problem is
>>>>> directory="$job_name". Galaxy expects to collect files from the job's
>>>>> working directory - basically the current working directory the job runs
>>>>> in. The directory= argument doesn't have variables expanded as far as I
>>>>> can
>>>>> tell. In any event it is used in walk_over_extra_files() that is in
>>>>> lib/galaxy/tools/parameters/output_collect.py - if you look there you see
>>>>> that it is simply appended to the job's working directory.
>>>>>
>>>>> So if you use:
>>>>>
>>>>> <discover_datasets pattern="(?P<name>.*)\.txt" />
>>>>>
>>>>> (note the < and > - this is effectively the regexp
>>>>> r"(?P<name>.*)\.txt" with the < and > escaped out)
>>>>>
>>>>> And alter the code so that it just writes files to the current
>>>>> directory, then you'll pick up the files one.txt, two,txt and three.txt.
>>>>>
>>>>> Peter
>>>>>
>>>>> On 20 October 2015 at 12:28, Steve Cassidy <steve.cass...@mq.edu.au>
>>>>> wrote:
>>>>>
>>>>>> Sorry, it was just an example of a tool that works - the file that it
>>>>>> writes out is put into that directory, so I assume that's where my files
>>>>>> should end up too.
>>>>>>
>>>>>> Steve
>>>>>>
>>>>>> On 20 October 2015 at 21:12, Peter van Heusden <p...@sanbi.ac.za>
>>>>>> wrote:
>>>>>>
>>>>>>> Sorry, I don't understand - what does the Upload File tool have to
>>>>>>> do with this?
>>>>>>>
>>>>>>> On 20 October 2015 at 11:49, Steve Cassidy <steve.cass...@mq.edu.au>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Yes, I'm sure that's where the problem lies. Writing out to the
>>>>>>>> current directory doesn't work. The files get written to
>>>>>>>> 'job_working_directory/000/1/' but if I run the Upload File tool the
>>>>>>>> result
>>>>>>>> is placed in 'files/000/'. I think I need to work out where to write
>>>>>>>> the
>>>>>>>> files, I found some references to $__new_file_path__ but that doesn't
>>>>>>>> seem
>>>>>>>> to help.
>>>>>>>>
>>>>>>>> Steve
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 20 October 2015 at 19:57, Peter van Heusden <p...@sanbi.ac.za>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I suspect that the problem might be in the <discover_datasets>
>>>>>>>>> then. I'm not an export on this, but "__name_and_ext__" turns into the
>>>>>>>>> regexp r"(?P<name>.*)\.(?P<ext>[^\.]+)?" in
>>>>>>>>> lib/galaxy/tools/parameters/output_collect.py, and is used by the
>>>>>>>>> DatasetCollector (line 358). This looks like it should match the
>>>>>>>>> filenames
>>>>>>>>> you're creating, but I'm not 100% sure how that code works. One thing
>>>>>>>>> I
>>>>>>>>> notice is the "directory" argument. If you write jobs to the current
>>>>>>>>> directory instead of "output_path" can you get it to work?
>>>>>>>>>
>>>>>>>>> Peter
>>>>>>>>>
>>>>>>>>> On 20 October 2015 at 09:52, Steve Cassidy <
>>>>>>>>> steve.cass...@mq.edu.au> wrote:
>>>>>>>>>
>>>>>>>>>> Thanks Peter,
>>>>>>>>>> I did see that proviso somewhere but no, refreshing doesn't
>>>>>>>>>> help.
>>>>>>>>>>
>>>>>>>>>> That page was one of those that I referred to getting to this
>>>>>>>>>> point.
>>>>>>>>>>
>>>>>>>>>> Steve
>>>>>>>>>>
>>>>>>>>>> On 20 October 2015 at 18:33, Peter van Heusden <p...@sanbi.ac.za>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Just a quick check - did you refresh your history to confirm
>>>>>>>>>>> that the dataset *is* empty? We had the same thing at SANBI but it
>>>>>>>>>>> turns
>>>>>>>>>>> out that Galaxy creates an empty output collection and then only
>>>>>>>>>>> populates
>>>>>>>>>>> it sometime after job completion (this is a know UI bug).
>>>>>>>>>>>
>>>>>>>>>>> See:
>>>>>>>>>>> http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collections/
>>>>>>>>>>>
>>>>>>>>>>> On 20 October 2015 at 08:48, Steve Cassidy <
>>>>>>>>>>> steve.cass...@mq.edu.au> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi all,
>>>>>>>>>>>> I'm trying to understand how to write a tool that generates a
>>>>>>>>>>>> dataset rather than a single output file. I've tried following
>>>>>>>>>>>> all of the
>>>>>>>>>>>> examples but I'm stuck, so I thought I would distil down the
>>>>>>>>>>>> simplest
>>>>>>>>>>>> example I could write and ask for help here.
>>>>>>>>>>>>
>>>>>>>>>>>> So here's my example:
>>>>>>>>>>>>
>>>>>>>>>>>> https://gist.github.com/stevecassidy/0fa45ad5853faacb5f55
>>>>>>>>>>>>
>>>>>>>>>>>> it's a simple python script that writes three files to a
>>>>>>>>>>>> directory named for the single input parameter.
>>>>>>>>>>>>
>>>>>>>>>>>> I think one of the problems I'm having is knowing where to
>>>>>>>>>>>> write the output to. I've run this under planemo serve and the job
>>>>>>>>>>>> runs,
>>>>>>>>>>>> creating the output directory within the
>>>>>>>>>>>> 'job_working_directory/000/1/SampleDataset' directory, however my
>>>>>>>>>>>> dataset
>>>>>>>>>>>> doesn't contain anything so clearly my outputs directive isn't
>>>>>>>>>>>> working:
>>>>>>>>>>>>
>>>>>>>>>>>> <outputs>
>>>>>>>>>>>> <collection type="list" label="$job_name"
>>>>>>>>>>>> name="output1">
>>>>>>>>>>>> <discover_datasets pattern="__name_and_ext__"
>>>>>>>>>>>> directory="$job_name" />
>>>>>>>>>>>> </collection>
>>>>>>>>>>>> </outputs>
>>>>>>>>>>>>
>>>>>>>>>>>> ($job_name is the name of the directory that is being written
>>>>>>>>>>>> to, SampleDataset in this case)
>>>>>>>>>>>>
>>>>>>>>>>>> Any help in getting this example working would be appreciated.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Steve
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Department of Computing, Macquarie University
>>>>>>>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>>>>>>>
>>>>>>>>>>>> ___________________________________________________________
>>>>>>>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>>>>>>>>
>>>>>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ___________________________________________________________
>>>>>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>>>>>> in your mail client. To manage your subscriptions to this
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>>>>>>>>>>> https://lists.galaxyproject.org/
>>>>>>>>>>>
>>>>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Department of Computing, Macquarie University
>>>>>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ___________________________________________________________
>>>>>>>>> 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:
>>>>>>>>> https://lists.galaxyproject.org/
>>>>>>>>>
>>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Department of Computing, Macquarie University
>>>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Department of Computing, Macquarie University
>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client. To manage your subscriptions to this
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>>>>> https://lists.galaxyproject.org/
>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Department of Computing, Macquarie University
>>>> http://web.science.mq.edu.au/~cassidy/
>>>>
>>>
>>>
>>
>>
>> --
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy/
>>
>
>
> ___________________________________________________________
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--
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
___________________________________________________________
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