removed specific version for python and for snakeobjects

Dockerfile

@@ -1,34 +1,16 @@
-FROM bitnami/minideb:buster
-MAINTAINER Boris Yamrom <[email protected]>
-ADD . /tmp/repo
-WORKDIR /tmp/repo
-ENV PATH /opt/conda/bin:${PATH}
-ENV LANG C.UTF-8
-ENV SHELL /bin/bash
+FROM bitnami/minideb:bullseye
+
 RUN install_packages wget curl bzip2 ca-certificates gnupg2 squashfs-tools git
+
 RUN /bin/bash -c "curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh && \
     bash miniconda.sh -b -p /opt/conda && \
     rm miniconda.sh"
-
-RUN /bin/bash -c "conda install -y -c conda-forge mamba &&                 \
-    mamba create -q -y -c iossifovlab                                      \
-    -c bioconda -c conda-forge -n snakeobjects snakeobjects --only-deps && \
-    source activate snakeobjects &&                                        \
-    mamba install -q -y -c conda-forge singularity &&                      \
-    conda clean --all -y &&                                                \
-    which python &&                                                        \
-    pip install .[reports,messaging,google-cloud]"
+ENV PATH /opt/conda/bin:${PATH}
 
+RUN /bin/bash -c "conda install -y -c conda-forge mamba                            && \
+    mamba create -q -y -n snakeobjects -c iossifovlab -c bioconda -c conda-forge snakeobjects singularity && \
+    conda clean --all -y                                                           && \
+    which python"
 
-# Make RUN commands use the new environment:
-RUN echo "conda activate snakeobjects" >> ~/.bashrc
-RUN echo "export PATH=/workdir/workflow:$PATH" >> ~/.bashrc
 ENV PATH /opt/conda/envs/snakeobjects/bin:${PATH}
-ENV SO_PIPELINE /workdir/workflow
-ENV SO_PROJECT .
-ENV SO_CONTAINER "yes"
-SHELL ["/bin/bash", "--login", "-c"]
-
-
-
 

conda.recipe/meta.yaml

@@ -33,7 +33,7 @@ requirements:
     - pip
   run:
     - python
-    - snakemake-minimal>=6.3
+    - snakemake-minimal
     # dependencies are defined in setup.py
     {% for dep in data['install_requires'] %}
     - {{ dep.lower() }}
@@ -46,7 +46,7 @@ test:
   requires:
     - pytest
     - pytest-cov
-    - snakemake-minimal>=6.3
+    - snakemake-minimal
   commands:
     - pytest tests