adding hisat2 and subread

berkeley-dsep-infra · Oct 21, 2024 · b436264 · b436264
1 parent d1fbe96
commit b436264
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -152,10 +152,10 @@ 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
-RUN rm /tmp/install-mambaforge.bash
+COPY install-miniforge.bash /tmp/install-miniforge.bash
+RUN chmod 777 /tmp/install-miniforge.bash
+RUN /tmp/install-miniforge.bash
+RUN rm /tmp/install-miniforge.bash
 
 USER ${NB_USER}
 

diff --git a/environment.yml b/environment.yml
@@ -28,8 +28,8 @@ dependencies:
 - fastqc=0.11.9
 - phyml=3.3.20200621
 - sra-tools=2.11
-# - hisat2=2.2.1
-# - subread=2.0.1
+- hisat2=2.2.1
+- subread=2.0.6
 - plink=1.90b6.21
 
 - syncthing==1.18.6

diff --git a/install-mambaforge.bash → install-miniforge.bash b/install-mambaforge.bash → install-miniforge.bash
@@ -3,10 +3,10 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION='24.3.0-0'
+MINIFORGE_VERSION='24.7.1-2'
 
-URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
-INSTALLER_PATH=/tmp/mambaforge-installer.sh
+URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/miniforge-installer.sh
 
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}