On Mon, Aug 26, 2013 at 12:27 PM, Carlos Borroto
<carlos.borr...@gmail.com> wrote:
> Hi,
>
> I'm interested in developing a tool that would allow easy interaction
> with the Galaxy API. I started coding and this[1] is what I have so
> far.
>
> [1]https://github.com/cjav/galaxy-api-tools
>
Second effort session on this project. The first time around I somehow
missed Bioblend python library, I made sure this is not the case this
time around. Bioblend is making development quite easy and is opening
a bunch of possibilities I didn't even know were possible.
The project is now also on pypi, all you need to install it is:
$ pip install galaxy-api-tools
This is a use case fully supported currently.
- List all workflows available to you:
$ galaxy-api-tools get-workflows
[ { u'id': u'f597429621d6eb2b',
u'model_class': u'StoredWorkflow',
u'name': u'Map and Variant Calling',
u'published': False,
u'tags': [],
u'url': u'/api/workflows/f597429621d6eb2b'},
{ u'id': u'f2db41e1fa331b3e',
u'model_class': u'StoredWorkflow',
u'name': u'Combine and Split',
u'published': False,
u'tags': [],
u'url': u'/api/workflows/f2db41e1fa331b3e'}]
- Show workflow details so you can clearly see what to expect and what
you need to provide:
$ galaxy-api-tools show-workflow name="Combine and Split"
{ u'id': u'f2db41e1fa331b3e',
u'inputs': { u'5': { u'label': u'FASTA', u'value': u''},
u'6': { u'label': u'QUAL', u'value': u''},
u'7': { u'label': u'BARCODE_INDEX', u'value': u''}},
u'model_class': u'StoredWorkflow',
u'name': u'Combine and Split',
u'published': False,
u'steps': { u'5': { u'id': 5,
u'input_steps': { },
u'tool_id': None,
u'type': u'data_input'},
u'6': { u'id': 6,
u'input_steps': { },
u'tool_id': None,
u'type': u'data_input'},
u'7': { u'id': 7,
u'input_steps': { },
u'tool_id': None,
u'type': u'data_input'},
u'8': { u'id': 8,
u'input_steps': { u'fasta_file': {
u'source_step': 5,
u'step_output': u'output'},
u'qual_file': {
u'source_step': 6,
u'step_output': u'output'}},
u'tool_id': u'fastq_combiner',
u'type': u'tool'},
u'9': { u'id': 9,
u'input_steps': { u'barcode_index': {
u'source_step': 7,
u'step_output': u'output'},
u'input_format|inputs_0|input': { u'source_step': 8,
u'step_output': u'output_file'}},
u'tool_id': u'ngs-tools_split_by_barcode',
u'type': u'tool'}},
u'tags': [],
u'url': u'/api/workflows/f2db41e1fa331b3e'}
- Upload two pairs of FNA/QUAL files from a 454 run and run the
previous workflow for combining them into a FASTQ file and split them
by barcode:
$ galaxy-api-tools upload --library name="API Imports" --upload-method
galaxy_filesystem \
--genome hg19 --folder "Run 20130918" --workflow name="Combine and Split" \
--add-file .qual=qual454=QUAL --workflow-input
BARCODE_INDEX=1cd8e2f6b131e891=ldda \
--workflow-param ngs-tools_split_by_barcode=barcodes=RL001,RL002 \
/local/seq_data/R_2013_09_18/1.fna /local/seq_data/R_2013_09_18/2.fna
{ u'history': u'0c5ffef6d88a1e97',
u'outputs': [u'1a5b83933dc4bf08', u'aebaa141e7243ebf']}
{ u'history': u'911dde3ddb677bcd',
u'outputs': [u'07a38ebd55a6989d', u'56fc5a09f8ae2546']}
There are a few issues I need to workout. Also, a lot of code
refactoring and commenting needs to happen if a seriously want other
people to join this effort. Ideally something like this could be built
inside Bioblend.
I hope someone else finds it useful,
Carlos
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