update install.sh

IntelLabs · Oct 10, 2024 · 8797dbc · 8797dbc
1 parent 8c2046b
commit 8797dbc
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/pipelines/fq2sortedbam/Dockerfile b/pipelines/fq2sortedbam/Dockerfile
@@ -30,12 +30,16 @@ WORKDIR Open-Omics-Acceleration-Framework/pipelines/fq2sortedbam
 #RUN git checkout e4cae79
 
 RUN bash install.sh onprem
-RUN echo "source ./miniforge3/bin/activate fq2bam" > ~/.bashrc
+RUN ln -s ./miniforge3 /opt/miniforge3
+ENV PATH=/opt/miniforge3/bin/:$PATH
+RUN echo "source /opt/miniforge3/bin/activate fq2bam" >> ~/.bashrc
+ENV source ~/.bashrc
+#RUN /bin/bash -c "opt/miniforge3/bin/activate fq2bam"
 
 RUN mkdir /input
 RUN mkdir /out
 RUN mkdir /refdir
 RUN mkdir /tempdir
 
-CMD bash
+CMD ["/bin/bash"]
 
diff --git a/pipelines/fq2sortedbam/install.sh b/pipelines/fq2sortedbam/install.sh
@@ -21,14 +21,14 @@ fi
 
 echo "Downloading and setting up miniconda..."
 [[ ! -e "Miniforge3-24.3.0-0-Linux-x86_64.sh" ]] && wget https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Miniforge3-24.3.0-0-Linux-x86_64.sh
-bash ./Miniforge3-24.3.0-0-Linux-x86_64.sh -u -b -p ./miniforge3
+bash ./Miniforge3-24.3.0-0-Linux-x86_64.sh -u -b -p ~/miniforge3
 
 echo "Setting up conda env named with given argument"
-./miniforge3/bin/conda env create --name fq2bam -f environment.yml
+~/miniforge3/bin/conda env create --name fq2bam -f environment.yml
 echo "Setting up conda env named new_env...DONE"
 
 echo "Activating conda env..."
-source ./miniforge3/bin/activate fq2bam
+source ~t /miniforge3/bin/activate fq2bam
 
 #echo "Downloading and setting up miniconda..."
 #if [ ! -e "Miniconda3-py39_23.3.1-0-Linux-x86_64.sh" ]