Merge pull request #3008 from felder/felder_biology_2934

Moving requirements.txt to environment.yml for biology issue #2934
berkeley-dsep-infra · Nov 17, 2021 · 4a99ccb · 4a99ccb
2 parents 5236bbe + faeb031
commit 4a99ccb
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Showing 3 changed files with 13 additions and 14 deletions.
diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -1,7 +1,7 @@
 FROM buildpack-deps:focal-scm
 
-ENV TZ=UTC
-RUN ln -snf /usr/share/zoneinfo/Etc/$TZ /etc/localtime && echo $TZ > /etc/timezone
+ENV TZ=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
 ENV LC_ALL en_US.UTF-8
 ENV LANG en_US.UTF-8
@@ -172,7 +172,6 @@ RUN apt-get update -qq --yes && \
 USER ${NB_USER}
 
 COPY environment.yml /tmp/
-COPY requirements.txt /tmp/
 COPY infra-requirements.txt /tmp/
 
 RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -37,5 +37,15 @@ dependencies:
 - raxml=8.2.*
 - muscle=3.8.*
 - dendropy=4.4.*
+
+# pedagogy packages
+- scipy==1.7.1
+- pandas==1.3.2
+- seaborn==0.11.2
+
+# For https://github.com/berkeley-dsep-infra/datahub/issues/1846
+# Conda does not have these 
 - pip:
-  - -r requirements.txt
+  - geonomics==1.1.9
+  - nlmpy==1.0.1
+  - -r infra-requirements.txt
diff --git a/deployments/biology/image/requirements.txt b/deployments/biology/image/requirements.txt