repo2docker local build passed the mamba/pip installation phase

berkeley-dsep-infra · Nov 9, 2023 · 8967bf4 · 8967bf4
1 parent e58e803
commit 8967bf4
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Showing 3 changed files with 3 additions and 10 deletions.
diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -180,10 +180,6 @@ COPY rsession.conf /etc/rstudio/rsession.conf
 # Use simpler locking strategy
 COPY file-locks /etc/rstudio/file-locks
 
-#install rsession proxy
-RUN pip install --no-cache-dir \
-        jupyter-rsession-proxy==2.0.1
-
 # Install IRKernel
 RUN r -e "install.packages('IRkernel', version='1.2')" && \
     r -e "IRkernel::installspec(prefix='${CONDA_DIR}')"

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -13,7 +13,7 @@ dependencies:
 - samtools=1.3.1
 - mafft=7.471
 - emboss=6.6.0
-- augustus=3.3.3
+- augustus=3.5.0
 - raxml-ng=1.0.1
 - structure=2.3.4
 - paml=4.9
@@ -69,3 +69,4 @@ dependencies:
 # Packages for MCB-160L iss #3942
   - allensdk==2.13.6
   - otter-grader==3.1.4
+  - jupyter-rsession-proxy==2.0.1
diff --git a/deployments/biology/image/install-mambaforge.bash b/deployments/biology/image/install-mambaforge.bash
@@ -3,15 +3,11 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=4.10.3-7
+MAMBAFORGE_VERSION='23.1.0-1'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
 
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-unset HOME
-
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}