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Using remote test data feature. Configurable conda channels. #54

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merged 5 commits into from
Mar 26, 2024
Merged

Using remote test data feature. Configurable conda channels. #54

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99e6c7d
configurable conda channels
dsavchenko Mar 11, 2024
814ea3e
use remote test files
dsavchenko Mar 11, 2024
2a6d777
path with sha not branch
dsavchenko Mar 11, 2024
cdb5e94
conda channels conf type
dsavchenko Mar 15, 2024
bedff77
Update Dockerfile_galaxy
dsavchenko Mar 26, 2024
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2 changes: 1 addition & 1 deletion Dockerfile_galaxy
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ FROM python:3.9

COPY . /source

# RUN pip install git+https://github.com/oda-hub/nb2workflow@master#egg=nb2workflow[galaxy]
RUN pip install git+https://github.com/oda-hub/nb2workflow@master#egg=nb2workflow[galaxy]
RUN pip install /source[galaxy] && rm -r /source

# Add Tini
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28 changes: 19 additions & 9 deletions odabot/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@

import click
from dynaconf import Dynaconf
from dynaconf.vendor.box import BoxList

logger = logging.getLogger()

Expand Down Expand Up @@ -684,6 +685,11 @@ def make_galaxy_tools(obj, dry_run, loop, force, pattern):
git_name = obj['settings'].get('nb2galaxy.git_identity.name', 'ODA bot')
git_email = obj['settings'].get('nb2galaxy.git_identity.email', '[email protected]')
git_credentials = obj['settings'].get('nb2galaxy.git_credentials', os.path.join(os.environ.get('HOME', '/'), '.git-credentials'))
available_channels = obj['settings'].get('nb2galaxy.conda_channels', ['conda-forge'])
if isinstance(available_channels, BoxList):
available_channels = available_channels.to_list()
elif isinstance(available_channels, str):
available_channels = available_channels.split(',')

repo_cache_dir = os.path.abspath(repo_cache_dir)
state_storage = os.path.abspath(state_storage)
Expand Down Expand Up @@ -834,16 +840,20 @@ def repo_file_path_if_available(filename):
outd = os.path.join(tools_repo_dir, 'tools', project['path'])
shutil.rmtree(outd, ignore_errors=True)

repo_files_baseurl = f"{project['web_url']}/-/raw/{last_commit['id']}/"

to_galaxy(input_path=wf_repo_dir,
toolname=tool_name,
out_dir=outd,
tool_version=new_version,
tool_id=tool_id,
requirements_file=req_file,
conda_environment_file=env_file,
citations_bibfile=bib_file,
help_file=help_file
)
toolname=tool_name,
out_dir=outd,
tool_version=new_version,
tool_id=tool_id,
requirements_file=req_file,
conda_environment_file=env_file,
citations_bibfile=bib_file,
help_file=help_file,
available_channels=available_channels,
test_data_baseurl=repo_files_baseurl
)

# creating shed file
if os.path.isfile(os.path.join(wf_repo_dir, '.shed.yml')):
Expand Down
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