Testing .gitpod.yml

.gitpod.yml

@@ -1,15 +1,24 @@
 tasks:
   - name: Setup Conda Environment
     init: |
+      # Set up paths and environment variables
       export PATH=$PATH:/home/gitpod/.pyenv/versions/3.12.6/bin
-      export PATH=$PATH:~/mirtop_env/bin
-      echo "export PATH=\$PATH:~/mirtop_env/bin" >> ~/.bashrc
-      echo "export PATH=\$PATH:/home/gitpod/.pyenv/versions/3.12.6/bin" >> ~/.bashrc
       wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O ~/miniconda.sh
-      bash ~/miniconda.sh -b -p ~/mirtop_env
+      bash ~/miniconda.sh -b -p ~/miniconda3
+      export PATH="$HOME/miniconda3/bin:$PATH"
+      echo "export PATH=\$PATH:$HOME/miniconda3/bin" >> ~/.bashrc
       conda config --set ssl_verify false  # For Gitpod compatibility
-      conda install anaconda-client -y
-      conda install -c bioconda samtools pybedtools -y
+
+      # Create a new Conda environment with Python 3.12 and install packages
+      conda create -y -n mirtop_env python=3.12
+      source activate mirtop_env
+      conda install -y -c bioconda samtools pybedtools
       pip install pytest pyyaml six pysam pandas biopython
+      
+      # Make the environment available on startup
+      echo "source activate mirtop_env" >> ~/.bashrc
+
     command: |
-      python setup.py develop
+      # Ensure the environment is activated and run the setup command
+      source activate mirtop_env
+      python setup.py develop