Fixed dockerfile

Dockerfile

@@ -1,39 +1,35 @@
-FROM continuumio/miniconda
+FROM continuumio/miniconda3
 
-RUN apt-get  --allow-releaseinfo-change update -t oldoldstable && apt-get install -y \
-    build-essential \
-    bzip2 \
-    ca-certificates \
-    git \
-    libglib2.0-0 \
-    libsm6 \
-    libxext6 \
-    libxrender1 \
-    mariadb-server \
-    mariadb-client \
-    wget \
-    zlib1g-dev \
-    procps \
+RUN apt-get update \
+    && apt-get install -y \
+        build-essential \
+        bzip2 \
+        ca-certificates \
+        git \
+        libglib2.0-0 \
+        libsm6 \
+        libxext6 \
+        libxrender1 \
+        mariadb-server \
+        mariadb-client \
+        wget \
+        zlib1g-dev \
+        procps \
     && rm -rf /var/lib/apt/lists/*
 
-RUN conda install -c daler \
-    pip \
-    cython \
-    matplotlib \
-    nose \
-    numpydoc \
-    pip \
-    pandas \
-    pyyaml \
-    sphinx \
-    pysam \
+RUN conda install -c bioconda -c conda-forge -c anaconda \
     colorama \
-    termcolor
-RUN conda install -c daler \
-    tabix \
-    bedtools=2.25.0
+    termcolor \
+    docopt 
+
+RUN conda install -c bioconda -c conda-forge -c anaconda \
+    pandas \
+    pybedtools
+
+RUN conda install -c bioconda -c conda-forge -c anaconda \
+    samtools
 ENV DISPLAY=:0
-ENV LANG C.UTF-8
+ENV LANG=C.UTF-8
 WORKDIR /opt/pybedtools
 
 RUN pip install https://github.com/AndersenLab/bam-toolbox/archive/1.0.0.tar.gz

bam/coverage.py

@@ -202,7 +202,6 @@ def calc_coverage(bamfile, regions=None, mtchr=None):
             Calculate coverage genome wide
         """
         bam = args["<bam>"]
-        print(b.contig_regions, file=sys.stderr)
         cov = calc_coverage(b, b.contig_regions)
 
         # Genomewide depth