In [27]:

    

from bioblend.galaxy import GalaxyInstance

# API access is only possible for registered users.
# Unregistered users can use the webinterface of https://hicexplorer.usegalaxy.eu

API_KEY = ""
gi = GalaxyInstance(url='https://hicexplorer.usegalaxy.eu', key=API_KEY)


    

In [2]:

    

# Create a history
history_id = gi.histories.create_history('Hi-C example NAR 2020')['id']


    

In [3]:

    

# Upload a dataset from an URL
upload = gi.tools.put_url('https://zenodo.org/record/1183661/files/HiC_S2_1p_10min_lowU_R1.fastq.gz', history_id, file_name='R1.fastq', file_type='fastqsanger.gz')


    

In [11]:

    

# get the uploaded dataset ids
# wait until the data has been uploaded
dataset_ids = []

all_items = gi.histories.show_history(history_id, contents=False)['state_ids']['ok']

datatype = 'fastqsanger.gz'
# get the files with the correct data type
for items in all_items:
    items_data = gi.datasets.show_dataset(items)
    if items_data['extension'] == datatype:
        dataset_ids.append(items)


    

In [12]:

    

# get the correct bowtie version
all_versions = gi.tools.get_tools(name='Bowtie2')
latest_version = None
latest_version_id = None
latest_version_number = '2.3.4.3+galaxy0'
for tool in all_versions:
    if tool['version'] == latest_version_number:
        latest_version = tool
        latest_version_id = latest_version['id']


    

In [ ]:

    

# prepare bowtie input


    

In [13]:

    

from bioblend.galaxy.tools.inputs import inputs, dataset


    

In [14]:

    

# run mapping

my_input = inputs().set("inputName",'value').set("input",dataset(dataset_ids[0]))

job_run = gi.tools.run_tool(history_id, latest_version_id, tool_inputs=my_input)


    

In [26]:

    

# get the computed dataset ids
# wait until the data has been computed
dataset_ids = []

all_items = gi.histories.show_history(history_id, contents=False)['state_ids']['ok']

datatype = 'fastqsanger.gz'
# get the files with the correct data type
for items in all_items:
    items_data = gi.datasets.show_dataset(items)
#     print(items_data)
    if items_data['extension'] == datatype:
        dataset_ids.append(items)


    

In [ ]:

    

# Download data


    

In [25]:

    

import os
download_path = 'download_galaxy'

os.mkdir(download_path)
gi.datasets.download_dataset(dataset_ids[0], file_path=download_path)


    

    
Out[25]:





'download_galaxy/Galaxy1-[R1.fastq].fastqsanger.gz'