use remote test files

oda-hub · Mar 11, 2024 · 814ea3e · 814ea3e
1 parent 99e6c7d
commit 814ea3e
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diff --git a/Dockerfile_galaxy b/Dockerfile_galaxy
@@ -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@galaxy-tool-test-remotefile#egg=nb2workflow[galaxy]
 RUN pip install /source[galaxy] && rm -r /source
 
 # Add Tini

diff --git a/odabot/cli.py b/odabot/cli.py
@@ -835,6 +835,8 @@ 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/{project['default_branch']}/"
+
                             to_galaxy(input_path=wf_repo_dir, 
                                       toolname=tool_name,
                                       out_dir=outd,
@@ -845,6 +847,7 @@ def repo_file_path_if_available(filename):
                                       citations_bibfile=bib_file,
                                       help_file=help_file,
                                       available_channels=available_channels,
+                                      test_data_baseurl=repo_files_baseurl
                                       )
 
                             # creating shed file