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nanoporetech / pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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ImportError: cannot import name 'parse_uri' #18

Closed Payam-Ebadi closed 3 years ago

Payam-Ebadi commented 3 years ago

Hello everyone, Can somebody help me with this error on PSV:

File "/home/grid/miniconda3/envs/pipeline-structural-variation-v2/lib/python3.6/site-packages/snakemake/init.py", line 593, in snakemake snakefile, overwrite_first_rule=True, print_compilation=print_compilation File "/home/grid/miniconda3/envs/pipeline-structural-variation-v2/lib/python3.6/site-packages/snakemake/workflow.py", line 1083, in include if is_local_file(snakefile): File "/home/grid/miniconda3/envs/pipeline-structural-variation-v2/lib/python3.6/site-packages/snakemake/common.py", line 65, in is_local_file from smart_open import parse_uri ImportError: cannot import name 'parse_uri'

I appreciate if someone give me an answer for this.

hannahgoldswain commented 3 years ago

I am also stuck here and would appreciate some help!

hannahgoldswain commented 3 years ago

Hi, I think you have to install smart_open, I installed it with conda install.

Hope it works, it got past that error for me!

cjw85 commented 3 years ago

Hi @hannahgoldswain,

Thank you for reporting this. It doesn't look like an error with the pipeline-sv code per se, rather with the snakemake package and its use of the smart_open pacakge. I will make smart_open a direct dependency of the pipeline conde.

valerii-pokrytiuk commented 3 years ago

@Payam-Ebadi you have to install older version of smart_open -- the latest one doesn't allow to import parse_uri.

In my case conda install smart_open=3 worked

namronb commented 3 years ago

@Payam-Ebadi you have to install older version of smart_open -- the latest one doesn't allow to import parse_uri.

In my case conda install smart_open=3 worked

Thanks, the "=3" was what I was missing to make it work!