single cell pipeline fails at rule all due to problem with "csv-table" and snakemake version

[mmilek]

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]

probably related to sphinx-doc/sphinx#8487

[messersc]

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

[mmilek]

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'