diff --git a/atlas/atlas.py b/atlas/atlas.py index c52b5138..3e7ee05c 100644 --- a/atlas/atlas.py +++ b/atlas/atlas.py @@ -7,7 +7,7 @@ import click -from snakemake.common.configfile import load_configfile +from snakemake.io import load_configfile from .make_config import validate_config from .init.atlas_init import run_init # , run_init_sra diff --git a/atlas/make_config.py b/atlas/make_config.py index 3f21dcb8..96332497 100644 --- a/atlas/make_config.py +++ b/atlas/make_config.py @@ -1,6 +1,6 @@ from .default_values import * from snakemake.utils import update_config as snakemake_update_config -from snakemake.common.configfile import load_configfile +from snakemake.io import load_configfile import tempfile import sys import os diff --git a/atlasenv.yml b/atlasenv.yml index 4a4b32b4..c1ec80ea 100644 --- a/atlasenv.yml +++ b/atlasenv.yml @@ -3,14 +3,14 @@ channels: - bioconda - defaults dependencies: - - python =3.11 + - python >=3.8, < 3.12 - mamba - - bbmap >= 39.01 - - snakemake-minimal >= 8 - #- pygments - #- networkx - #- graphviz - - pandas =2 + - bbmap >= 39.01, <40 + - snakemake-minimal >= 7.18.1, <7.26 + - pygments + - networkx + - graphviz + - pandas >=1.2, <1.6 - pyarrow # for parquet reading - click >=7 - ruamel.yaml >=0.17