Update packages

atlas/atlas.py

@@ -7,7 +7,7 @@
 import click
 
 
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 from .make_config import validate_config
 from .init.atlas_init import run_init  # , run_init_sra
 
@@ -247,7 +247,7 @@ def run_download(db_dir, jobs, snakemake_args):
     cmd = (
         "snakemake --snakefile {snakefile} download "
         "--jobs {jobs} --rerun-incomplete "
-        "--conda-frontend mamba --scheduler greedy "
+        "--scheduler greedy "
         "--nolock  --use-conda  --conda-prefix {conda_prefix} "
         " --show-failed-logs "
         "--config database_dir='{db_dir}' {add_args} "

atlas/make_config.py

@@ -1,6 +1,6 @@
 from .default_values import *
 from snakemake.utils import update_config as snakemake_update_config
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import tempfile
 import sys
 import os

atlasenv.yml

@@ -3,10 +3,9 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python >=3.8, < 3.12
-  - mamba
+  - python >=3.11, < 3.12
   - bbmap >= 39.01, <40
-  - snakemake-minimal >= 7.18.1, <7.26
+  - snakemake-minimal >= 9.3.3, <10
   - pygments
   - networkx
   - graphviz

test/test_docker.sh

@@ -0,0 +1,9 @@
+#! /bin/bash
+
+pip install -e .
+
+atlas --help
+
+cd test
+
+./test_local.sh #--conda-frontend conda

workflow/envs/fasta.yaml

@@ -3,7 +3,7 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - pyfastx=0.9
+    - pyfastx=2.1
     - pandas=1.2
     - pyarrow
     - biopython

workflow/envs/instrain.yaml

@@ -3,5 +3,6 @@ channels:
 - bioconda
 - defaults
 dependencies:
-- instrain =1.5.*
-- pandas>=1.5,<2.0
+- instrain >=1.9, <2
+- python <3.12
+- samtools >=1.21, <2

workflow/envs/required_packages.yaml

@@ -10,3 +10,4 @@ dependencies:
     - pandas >=1.2, <2
     - samtools >=1.13, <2
     - sambamba >=1.0.1
+