Small fixes #206
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Small fixes #206
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bio-la
reviewed
Mar 4, 2024
| @@ -16,7 +16,7 @@ conda config --add channels conda-forge | |||
| conda config --set channel_priority strict | |||
| # you should remove the strict priority afterwards! | |||
| conda search r-base | |||
| conda create --name pipeline_env python=3.9 r-base=4.3.0 | |||
| conda create --name pipeline_env python=3.10 r-base=4.3.0 | |||
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just a reminder to test r-base 4.3.3
bio-la
requested changes
Mar 4, 2024
| @@ -338,8 +338,8 @@ def plot_marker_dotplots(marker_file, log_file, outfile, | |||
| """ | |||
| data_obj=PARAMS['sample_prefix'] + "_clustered.h5mu" | |||
| # check there is a figures directory | |||
| if not os.path.exists(fig_path): | |||
| os.makedirs(fig_path) | |||
| #if not os.path.exists(fig_path): | |||
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please reinstate this check, we need to make sure the pipeline doesn't fail for missing dirs
bio-la
approved these changes
Mar 5, 2024
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Hi!
Made some fixes while stress-testing the environment.
Also fixes DendrouLab/panpipes-tutorials#28 and DendrouLab/panpipes-tutorials#30
One weird error was that lines 341 and 342 in pipeline_clustering.py threw errors. If that is not reproducible, I can change it back.