1.4.0 dev m1 (#136)

* mods to Dockerfile * wip * update
artic-network · Aug 22, 2024 · ed69b82 · ed69b82
1 parent e6a0a16
commit ed69b82
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -21,8 +21,11 @@ USER root
 
 RUN python3 -m pip install ./fieldbioinformatics
 
+RUN pip uninstall -y tensorflow keras pyabpoa \
+  && micromamba install -y -c conda-forge -c bioconda tensorflow=2.11 keras=2.11
+
 USER $MAMBA_USER
 
 ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
 
-CMD ["/bin/bash"]
+CMD ["/bin/bash"]
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
+      - medaka==1.12.0