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update in tabulate leads to error when running pangolin #489
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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). |
We had the same error with our system Snakemake 6.12.3. Rolling back to tabulate==0.8.10 fixed the problem. |
Should be fixed in latest patch now- will try to keep an eye on when snakemake resolve their issue #1212 |
@aineniamh independent of the status of the snakemake issue you seem to have removed the offending |
Ah right, was that the part causing snakemake to error out? I'll look at changing to latest so |
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. |
I don't belive pangolin modifies the users bashrc, could you provide an example of what you mean? |
After running: 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)" |
Both of those are conda commands, so it looks like conda is modifying its own configuration, perhaps with the update command? |
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. |
There is a known issue with newer versions of tabulate that result in `AttributeError: 'str' object has no attribute 'name'` (see cov-lineages/pangolin#489). To resolve this error, environment specs have been modified to specify tabulate==0.8.10.
Hi all,
Snakemake is encountering this issue snakemake/snakemake#1899 which leads to this error when running pangolin:
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
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