On Mon, Aug 26, 2013 at 12:27 PM, Carlos Borroto carlos.borroto@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.
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