bio hub

berkeley-dsep-infra · May 7, 2024 · 1e34fbe · 1e34fbe
1 parent a92388b
commit 1e34fbe
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Showing 3 changed files with 19 additions and 19 deletions.
diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -123,10 +123,6 @@ RUN apt-get update -qq --yes > /dev/null && \
 
 WORKDIR /home/jovyan
 
-COPY install-mambaforge.bash /tmp/install-mambaforge.bash
-RUN chmod 777 /tmp/install-mambaforge.bash
-RUN /tmp/install-mambaforge.bash
-
 # Needed by RStudio
 RUN apt-get update -qq --yes && \
     apt-get install --yes --no-install-recommends -qq \
@@ -164,6 +160,10 @@ RUN apt-get update -qq --yes && \
     apt-get install --yes  -qq \
         libcurl4-openssl-dev > /dev/null
 
+COPY install-mambaforge.bash /tmp/install-mambaforge.bash
+RUN chmod 777 /tmp/install-mambaforge.bash
+RUN /tmp/install-mambaforge.bash
+
 USER ${NB_USER}
 
 COPY environment.yml /tmp/

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -2,9 +2,9 @@ channels:
 - bioconda
 - conda-forge
 dependencies:
-- python=3.9.*
+- python=3.11.*
 - pip=22.2.*
-
+# - statsmodels==0.14.1
 # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2)
 - nb_conda_kernels=2.3.1
 
@@ -34,10 +34,10 @@ dependencies:
 - syncthing==1.18.6
 
 # Packages for IB120/201/CCB210
-- sympy=1.6.2
+- sympy=1.12
 
 # Packages from bioconda for BioE-131, Fall 2020, Issue #1885
-- bowtie2=2.4.2
+# - bowtie2=2.5.3  # commented out by sknapp 2024.05.07 doesn't support py3.11
 - spades=3.14.1
 
 # Packages for MCB280A, Spring 2022
@@ -48,30 +48,30 @@ dependencies:
 - muscle=3.8.*
 - dendropy=4.4.*
 
-
 # pedagogy packages
-- scipy=1.7.1
-- pandas=1.3.2
+- scipy=1.11.
+- pandas=2.2.2
 - seaborn=0.11.2
 
 # compbio BioE c146, Fall 22 and into the future, issue 3785
-- scikit-learn=1.1.2
+- scikit-learn=1.2.2
 
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 
 # For https://github.com/berkeley-dsep-infra/datahub/issues/1846
 # Conda does not have these
 - pip:
+  - -r infra-requirements.txt
 # MCB280A, Spring 2022
-  - pybedtools==0.9.0
+  - pybedtools==0.10.0
 # removed for PR https://github.com/berkeley-dsep-infra/datahub/pull/4406 - macs2==2.2.7.1
-  - geonomics==1.1.9
-  - nlmpy==1.0.1
-  - datascience==0.17.5
-  - -r infra-requirements.txt
+  - geonomics==1.4.1
+  - nlmpy==1.2.0
+  - datascience==0.17.6
+
 # Packages for MCB-160L iss #3942
-  - allensdk==2.13.6
+  - allensdk==2.16.2
   - otter-grader==3.1.4
 # for exporting notebooks to pdf
   - nbconvert==7.6.0

diff --git a/deployments/biology/image/install-mambaforge.bash b/deployments/biology/image/install-mambaforge.bash
@@ -3,7 +3,7 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION='23.1.0-1'
+MAMBAFORGE_VERSION='24.3.0-0'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh