Updated several package versions to be compatible with python 3.8.6. Now iCount installs in conda via pip.

Author: grexor

Dockerfile

@@ -8,7 +8,9 @@ ENV TZ=Europe/Ljubljana
 # thanks to https://github.com/bschiffthaler/ngs/blob/master/base/Dockerfile
 # and https://github.com/AveraSD/ngs-docker-star/blob/master/Dockerfile
 
-SHELL ["/bin/bash", "-c"]
+SHELL ["/bin/bash", "--login", "-c"]
+
+RUN apt-get install -y vim
 
 RUN conda update -n base -c defaults conda -y
 RUN conda install -c conda-forge mamba -y
@@ -36,14 +38,20 @@ RUN chown -R icuser.icuser /home/icuser
 USER icuser
 WORKDIR /home/icuser
 RUN mkdir /home/icuser/storage
-RUN git clone https://github.com/tomazc/iCount.git --branch snakemake
+#RUN git clone https://github.com/tomazc/iCount.git --branch snakemake
+COPY . /home/icuser/iCount
 
 RUN conda create -c conda-forge -c bioconda -n iCount_pipeline3 -y
 RUN conda init bash
 RUN echo "conda activate iCount_pipeline3" >> ~/.bashrc
-#RUN conda env update --file iCount/conda_iCount.yaml # needs ~ 4 GB RAM, otherwise killed
-#RUN pip install ./iCount
 
-#ENV PATH /home/icuser/bin:$PATH
-#WORKDIR /home/icuser
-#CMD ["/bin/bash"]
+SHELL ["conda", "run", "-n", "iCount_pipeline3", "/bin/bash", "-c"]
+
+### needs ~ 4 GB RAM, otherwise killed
+RUN conda env update --file iCount/conda_iCount.yaml
+
+RUN pip install ./iCount
+
+ENV PATH /home/icuser/bin:$PATH
+WORKDIR /home/icuser
+CMD ["/bin/bash"]

conda_iCount.yaml

@@ -5,24 +5,23 @@ channels:
 
 dependencies:
   - python = 3.8.6
-  - snakemake = 5.5.4
-  - jinja2 = 2.10.1
-  - networkx = 2.3
-  - bcftools = 1.9
-  - samtools = 1.10
+  - snakemake = 5.28.0
+  - jinja2 = 2.11.2
+  - networkx = 2.5
+  - bcftools = 1.11
+  - samtools = 1.11
   - bwa = 0.7.17
-  - pysam = 0.16.0
-  - cutadapt = 2.4
-  - bedtools = 2.28
-  - STAR = 2.7.2a
-  - trim-galore = 0.6.4
+  - pysam = 0.16.0.1
+  - cutadapt = 3.0
+  - bedtools = 2.29.2
+  - STAR = 2.7.6a
+  - trim-galore = 0.6.6
   - pip = 20.2.4
-  - pybedtools = 0.8.0
-  - numpy = 1.17.1
-  - pandas = 0.25.1
-  - pybedtools = 0.8.0
-  - numpydoc = 0.9.1
-  - sphinx = 2.2.0
-  - matplotlib = 3.1.0
-  - docutils = 0.15.2
+  - pybedtools = 0.8.1
+  - numpy = 1.19.4
+  - pandas = 1.1.4
+  - numpydoc = 1.1.0
+  - sphinx = 3.3.1
+  - matplotlib = 3.3.3
+  - docutils = 0.16
   - sphinx-releases = 1.6.1