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bihealth / seasnap-pipeline

SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline
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single cell pipeline fails at rule all due to problem with "csv-table" and snakemake version #16

Open mmilek opened 2 years ago

mmilek commented 2 years ago

Using current conda envrinoment (conda_env.yaml), the single-cell pipeline on branch feature_cellranger_multi fails due to problems with csv-table directive path.

RuleException:
SystemMessage in line 94 of /data/gpfs-1/home/users/milekm_c/seasnap-pipeline/sc_pipeline.snake:
:17: (SEVERE/4) Problems with "csv-table" directive path:
[Errno 2] No such file or directory: '../sc_analysis/pipeline_report/all_samples.all_mates/out/pipeline_report.all_samples.all_mates.summary.csv'.

Most likely cause is that the current yaml file leads to the installation of higher version of snakemake (7.1.0), which fails with the csv-table. Workaround is to use the conda_env_mapping_sc.yaml on development branch, which will install snakemake 5.14.0.

bobermayer commented 2 years ago

probably related to https://github.com/sphinx-doc/sphinx/issues/8487

messersc commented 2 years ago

@mmilek can you please document which sphinx versions are present when installing snakemake 5 vs 7.

mmilek commented 2 years ago

might not be installed at all? working environment:

(sea_snap_bo_final) [milekm_c@hpc-cpu-219 python3.7]$ python -c 'import sphinx'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sphinx'

broken environment:

(sea_snap) [milekm_c@hpc-cpu-219 python3.7]$ python -c 'import sphinx'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sphinx'