quickstart tutorial command throws attribute error

[clb21565]

hi there,
running the quickstart tutorial command:
(grist) genome-grist run conf-tutorial.yml summarize_gather summarize_mapping

produces the following result/error:

samples: ['SRR5950647']
outdir: outputs.tutorial
base_tempdir: /tmp/tmpmav0xysu
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Traceback (most recent call last):
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/snakemake/init.py", line 699, in snakemake
success = workflow.execute(
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/snakemake/workflow.py", line 1056, in execute
logger.run_info("\n".join(dag.stats()))
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/snakemake/dag.py", line 2192, in stats
yield tabulate(rows, headers="keys")
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/tabulate/init.py", line 2048, in tabulate
list_of_lists, headers = _normalize_tabular_data(
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/tabulate/init.py", line 1471, in _normalize_tabular_data
rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/tabulate/init.py", line 1471, in
rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/tabulate/init.py", line 107, in _is_separating_line
(len(row) >= 1 and row[0] == SEPARATING_LINE)
File "/home/clb21565/miniconda3/envs/grist/lib/python3.9/site-packages/snakemake/rules.py", line 1127, in eq
return self.name == other.name and self.output == other.output
AttributeError: 'str' object has no attribute 'name'

things seemed to have installed OK

[clb21565]

turns out i didn't have snakemake installed as i believed i did, conda installed and all is well

[ctb]

that's an odd error if snakemake wasn't installed! hmm. please let me know if you run into any more problems!

[carden24]

I had the same issue when installing grist 0.9, i run conda install snakemake and it worked to bypass the error. however, I now have the issue #241

[ctb]

This error also popped up in spacegraphcats: spacegraphcats/spacegraphcats#471

It turns out the initial error was caused by installing tabulate v0.9.0, which was released on Oct 6, 2022; this broke snakemake v6.12.3, which relied on tabulate v0.8.10 but was not version pinned to that.

I confirmed this by:

• first, running the quickstart, and recapitulating the error above; pip show tabulate showed v0.9.0.

• then, upgrading snakemake to latest (7.18.2) and not having any problems.

• finally, forcing the original install via pip install snakemake==6.12.3 tabulate==0.8.10, and showing that the problem returned.

[ctb]

suggested fix: snakemake/snakemake#1989