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nanoporetech / pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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No module named 'boto3' #17

Open Payam-Ebadi opened 3 years ago

Payam-Ebadi commented 3 years ago

Hello Everyone Can somebody help me with the following error in 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 File "/home/grid/miniconda3/envs/pipeline-structural-variation-v2/lib/python3.6/site-packages/smart_open/init.py", line 1, in from .smart_open_lib import * File "/home/grid/miniconda3/envs/pipeline-structural-variation-v2/lib/python3.6/site-packages/smart_open/smart_open_lib.py", line 72, in import smart_open.s3 as smart_open_s3 File "/home/grid/miniconda3/envs/pipeline-structural-variation-v2/lib/python3.6/site-packages/smart_open/s3.py", line 3, in import boto3 ModuleNotFoundError: No module named 'boto3'

thank you very much.

Payam-Ebadi commented 3 years ago

Guys , I already found my answer:

Don't use sudo in a virtual environment because it ignores the environment's variables and therefore sudo pip refers to your global pip installation. So with your environment activated, rerun pip install boto3 but without sudo.