Conda yaml dev

Author: grexor

Dockerfile

@@ -8,28 +8,23 @@ 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"]
+
 RUN conda update -n base -c defaults conda -y
+RUN conda install -c conda-forge mamba -y
 
-RUN conda update -n base -c defaults conda
 RUN conda config --add channels defaults
 RUN conda config --add channels bioconda
 RUN conda config --add channels conda-forge
 
 ### samtools
-RUN conda install -c bioconda -y "samtools>=1.10"
+#RUN conda install -c bioconda -y "samtools>=1.10"
 
 ### bedtools, need at least version 2.26, where merge command reports strand
-RUN conda install -c bioconda -y bedtools
+# RUN conda install -c bioconda -y bedtools
 
 ### RNA-star
-RUN conda install -c bioconda -y star
-
-### numpy
-
-
-#USER root
-# to speed-up building of Docker images
-#RUN /home/icuser/.icountenv/bin/pip install numpy pandas pysam pybedtools numpydoc matplotlib
+# RUN conda install -c bioconda -y star
 
 #################
 #### iCount
@@ -45,15 +40,10 @@ RUN git clone https://github.com/tomazc/iCount.git --branch snakemake
 
 RUN conda create -c conda-forge -c bioconda -n iCount_pipeline3 -y
 RUN conda init bash
-RUN exec bash # restart shell
-RUN conda activate iCount_pipeline3
-RUN conda install -c conda-forge mamba -y
-RUN conda env update --file iCount/iCount/snakemake/envs/environment_iCount.yaml # needs ~ 4 GB RAM, otherwise killed
-
-USER root
-RUN echo "conda activate iCount_pipeline3" >> /etc/bash.bashrc
+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
 
-USER icuser
-ENV PATH /home/icuser/bin:$PATH
-WORKDIR /home/icuser
-CMD ["/bin/bash"]
+#ENV PATH /home/icuser/bin:$PATH
+#WORKDIR /home/icuser
+#CMD ["/bin/bash"]

conda_iCount.yaml

@@ -1,28 +1,28 @@
 channels:
+  - defaults
   - bioconda
   - conda-forge
 
 dependencies:
-  - snakemake =5.5.4
-  - python =3.8
-  - jinja2 =2.10.1
-  - networkx =2.3
-  - bcftools =1.9
-  - samtools
-  - bwa =0.7.17
-  - pysam = 0.14
-  - cutadapt =2.4
-  - bedtools =2.28
-  - STAR =2.7.2a
+  - python = 3.8.6
+  - snakemake = 5.5.4
+  - jinja2 = 2.10.1
+  - networkx = 2.3
+  - bcftools = 1.9
+  - samtools = 1.10
+  - bwa = 0.7.17
+  - pysam = 0.16.0
+  - cutadapt = 2.4
+  - bedtools = 2.28
+  - STAR = 2.7.2a
   - trim-galore = 0.6.4
-  - pip =19.2.3
-  - 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
+  - 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
-  - sphinx_rtd_theme =0.4.3
-  - sphinx-releases =1.6.1
+  - sphinx-releases = 1.6.1