From ed69b8290fd7656bfe48e4e00e9d3c1eb094d8f7 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Thu, 22 Aug 2024 10:59:22 +0100
Subject: [PATCH] 1.4.0 dev m1 (#136)

* mods to Dockerfile

* wip

* update
---
 Dockerfile      | 5 ++++-
 environment.yml | 5 +++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 272a109a..4bbe0ef7 100644
--- 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"]
\ No newline at end of file
+CMD ["/bin/bash"]
diff --git a/environment.yml b/environment.yml
index 3f0c52d1..6f90fecc 100644
--- 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
\ No newline at end of file
+      - medaka==1.12.0