Re: [galaxy-dev] 'galaxy-api-tools' project

18 Sep 2013

      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.
[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