From 8797dbccba325bfe9c60d6189bea816b2ebff354 Mon Sep 17 00:00:00 2001 From: Ubuntu Date: Thu, 10 Oct 2024 12:47:02 +0000 Subject: [PATCH] update install.sh --- pipelines/fq2sortedbam/Dockerfile | 8 ++++++-- pipelines/fq2sortedbam/install.sh | 6 +++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/pipelines/fq2sortedbam/Dockerfile b/pipelines/fq2sortedbam/Dockerfile index dba408b..6b1a8d2 100644 --- 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 index cbfe2ee..b0b8790 100755 --- 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" ]