wip

artic-network · Aug 21, 2024 · e211d2e · e211d2e
1 parent aa33d86
commit e211d2e
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -15,15 +15,15 @@ RUN sed -i 's/name: artic/name: base/' /tmp/env.yml
 RUN micromamba install --yes --file /tmp/env.yml && \
     micromamba clean --all --yes
 
-RUN pip uninstall -y tensorflow keras pyabpoa \
-  && conda install -y -c conda-forge tensorflow~=2.11 keras~=2.11
-
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 USER root
 
 RUN python3 -m pip install ./fieldbioinformatics
 
+RUN pip uninstall -y tensorflow keras pyabpoa \
+  && micromamba install -y -c conda-forge tensorflow~=2.11 keras~=2.11
+
 USER $MAMBA_USER
 
 ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]

diff --git a/environment.yml b/environment.yml
@@ -4,14 +4,15 @@ channels:
   - bioconda
   - defaults
 dependencies:
+  - python==3.9
   - longshot
   - bcftools
   - biopython
   - bwa
+  - clair3
   - clint
   - htslib
   - minimap2
-  - clair3
   - multiqc
   - muscle<5.1
   - pandas
@@ -25,4 +26,4 @@ dependencies:
   - samtools
   - tqdm
   - pip:
-    - medaka~=1.12.0
+      - medaka==1.12.0