update in tabulate leads to error when running pangolin

[abel-betraoui]

Hi all,

Snakemake is encountering this issue snakemake/snakemake#1899 which leads to this error when running pangolin:

Traceback (most recent call last):
  File "/opt/conda/envs/pangolin/lib/python3.10/site-packages/snakemake/__init__.py", line 699, in snakemake
    success = workflow.execute(
  File "/opt/conda/envs/pangolin/lib/python3.10/site-packages/snakemake/workflow.py", line 1043, in execute
    logger.run_info("\n".join(dag.stats()))
  File "/opt/conda/envs/pangolin/lib/python3.10/site-packages/snakemake/dag.py", line 2176, in stats
    yield tabulate(rows, headers="keys")
  File "/opt/conda/envs/pangolin/lib/python3.10/site-packages/tabulate/__init__.py", line 2048, in tabulate
    list_of_lists, headers = _normalize_tabular_data(
  File "/opt/conda/envs/pangolin/lib/python3.10/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 "/opt/conda/envs/pangolin/lib/python3.10/site-packages/tabulate/__init__.py", line 1471, in <lambda>
    rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
  File "/opt/conda/envs/pangolin/lib/python3.10/site-packages/tabulate/__init__.py", line 107, in _is_separating_line
    (len(row) >= 1 and row[0] == SEPARATING_LINE)
  File "/opt/conda/envs/pangolin/lib/python3.10/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'

Snakemake released version 7.15.2 which fixes the issue, however due to #313, snakemake version was set to <=6.8.0.

Note that falling back to tabular==0.8.10 fixes the problem but it might be better to catch up to snakemake's latest version.
Thanks

[aineniamh]

We pinned to snakemake<=6.8.0 because of the path handling issue. I wonder if that has been resolved in recent snakemake versions (this snakemake issue remains open: snakemake/snakemake#1212).

[xqinbcm]

We had the same error with our system Snakemake 6.12.3. Rolling back to tabulate==0.8.10 fixed the problem.
pip install tabulate==0.8.10

[aineniamh]

Should be fixed in latest patch now- will try to keep an eye on when snakemake resolve their issue #1212

[wm75]

@aineniamh independent of the status of the snakemake issue you seem to have removed the offending os.path.join attempts with workflow.current_basedir from pangolearn.smk as part of ff0a7e9.
So chances are that pinning snakemake is no longer required.

[aineniamh]

Ah right, was that the part causing snakemake to error out? I'll look at changing to latest so

[xqinbcm]

This version of pangolin also seems to change user's .bashrc to setup default conda to be conda3/envs/pangolin/bin/conda, which can cause other default conda-installed programs not to be able to found.

[aineniamh]

I don't belive pangolin modifies the users bashrc, could you provide an example of what you mean?

[xqinbcm]

After running:
conda activate pangolin
conda update pangolin

Got this appended to the .bashrc to reset default conda, but not sure what caused it:

>>> conda initialize >>>

!! Contents within this block are managed by 'conda init' !!

__conda_setup="$('/stornext/snfs130/covid-seq/xqin/covid19/bin/share/conda3/envs/pangolin/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/stornext/snfs130/covid-seq/xqin/covid19/bin/share/conda3/envs/pangolin/etc/profile.d/conda.sh" ]; then
. "/stornext/snfs130/covid-seq/xqin/covid19/bin/share/conda3/envs/pangolin/etc/profile.d/conda.sh"
else
export PATH="/stornext/snfs130/covid-seq/xqin/covid19/bin/share/conda3/envs/pangolin/bin:$PATH"
fi
fi
unset __conda_setup

[aineniamh]

Both of those are conda commands, so it looks like conda is modifying its own configuration, perhaps with the update command?

[sbridgett]

Thank you for explain how to fix this. I was getting the same error as in first post above about "AttributeError: 'str' object has no attribute 'name'". Upgrading to latest snakemake-minimal (snakemake-minimal-7.16.0 from the bioconda channel) fixed this problem. It has also removed a previous warning message about "Falling back to greedy scheduler because no default solver is found for pulp (you have to install either coincbc or glpk)", even though coin-or-cbc (2.10.7), coincbc (2.10.7) and glpk (5.0) were already installed in the same conda environment. Thank you.

Regarding that conda initialise, before reading about this issue about snakemake, I had thought that maybe updating to latest conda would fix the error, but after updating to latest conda 22.9.0, I lost the normal bash prompt, so found this issue: conda 22.9.0 breaks bash command prompt, explaining that "conda init bash" fixed this.