diff --git a/atlas/atlas.py b/atlas/atlas.py
index a1046a4d..cad6aeb5 100644
--- a/atlas/atlas.py
+++ b/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} "
diff --git a/atlas/make_config.py b/atlas/make_config.py
index e65025b7..a80c9323 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.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import tempfile
 import sys
 import os
diff --git a/atlasenv.yml b/atlasenv.yml
index c1ec80ea..bf1dfd8d 100644
--- a/atlasenv.yml
+++ b/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
diff --git a/test/test_docker.sh b/test/test_docker.sh
new file mode 100644
index 00000000..775881a1
--- /dev/null
+++ b/test/test_docker.sh
@@ -0,0 +1,9 @@
+#! /bin/bash
+
+pip install -e .
+
+atlas --help
+
+cd test
+
+./test_local.sh #--conda-frontend conda
\ No newline at end of file
diff --git a/workflow/envs/fasta.yaml b/workflow/envs/fasta.yaml
index 13fc46c2..7beaf1f7 100644
--- a/workflow/envs/fasta.yaml
+++ b/workflow/envs/fasta.yaml
@@ -3,7 +3,7 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - pyfastx=0.9
+    - pyfastx=2.1
     - pandas=1.2
     - pyarrow
     - biopython
diff --git a/workflow/envs/instrain.yaml b/workflow/envs/instrain.yaml
index f48da8e7..7e13450c 100644
--- a/workflow/envs/instrain.yaml
+++ b/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
diff --git a/workflow/envs/required_packages.yaml b/workflow/envs/required_packages.yaml
index deb891ae..9c7cb207 100644
--- a/workflow/envs/required_packages.yaml
+++ b/workflow/envs/required_packages.yaml
@@ -10,3 +10,4 @@ dependencies:
     - pandas >=1.2, <2
     - samtools >=1.13, <2
     - sambamba >=1.0.1
+