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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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micromamba snakemake import error #506

Closed akhilvelluva closed 8 months ago

akhilvelluva commented 9 months ago

I got error while running demo after the drop install using this command micromamba create -n drop_env -c conda-forge -c bioconda drop --override-channels

My path echo $PATH /home/akhil/micromamba/envs/drop_env/bin:/condabin:/software/anaconda3/2021.05/bin:/software/micromamba/1.4.9/bin:/opt/lsf/10.1/linux3.10-glibc2.17-x86_64/etc:/opt/lsf/10.1/linux3.10-glibc2.17-x86_64/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/lsf-shared/bin:/software/bin

which python

~/micromamba/envs/drop_env/bin/python

which snakemake

~/micromamba/envs/drop_env/bin/snakemake

drop demo Traceback (most recent call last): File "/home/akhil/micromamba/envs/drop_env/bin/drop", line 6, in from drop.cli import main File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/drop/init.py", line 1, in from .setupDrop import * File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/drop/setupDrop.py", line 2, in from drop.config.DropConfig import DropConfig File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/drop/config/init.py", line 1, in from .DropConfig import DropConfig File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/drop/config/DropConfig.py", line 1, in from .SampleAnnotation import SampleAnnotation File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/drop/config/SampleAnnotation.py", line 1, in from drop import utils File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/drop/utils.py", line 3, in import wbuild File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/wbuild/init.py", line 10, in from . import autolink File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/wbuild/autolink.py", line 6, in from wbuild.utils import Config File "/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/wbuild/utils.py", line 12, in from snakemake import get_argument_parser, parse_config, SNAKEFILE_CHOICES ImportError: cannot import name 'get_argument_parser' from 'snakemake' (/home/akhil/micromamba/envs/drop_env/lib/python3.12/site-packages/snakemake/init.py)

both python and snakemake loaded from same directory and how to resolve this ?

akhilvelluva commented 8 months ago

fixed using the yaml file

vyepez88 commented 8 months ago

Hi, sorry for the late reply, I was trying to google your error but couldn't find anything. Thanks also for reporting the solution!