installing samtools and GraphAligner from Bioconda

Dockerfile

@@ -8,15 +8,12 @@ LABEL about.home="https://github.com/pangenome/pgge"
 LABEL about.license="SPDX:MIT"
 
 # Required dependencies
-# samtools
-# TODO add samtools from Bioconda?
 RUN apt-get update \
         && apt-get install -y --no-install-recommends \
         wget \
         curl \
         less \
         gcc \ 
-        samtools \
         tzdata \
         make \
         git \
@@ -62,21 +59,6 @@ RUN wget \
 ENV PATH /miniconda/bin:$PATH
 SHELL ["/bin/bash", "-c"]
 
-# GraphAligner
-# Unfortunately, the current Bioconda version of GraphAligner emits a 15-column GAF, whereas the most recent commit on github emits a 16-column GAF
-# Therefore, we can't use the Bioconda version as of now
-RUN git clone --recursive https://github.com/maickrau/GraphAligner \
-        && cd GraphAligner \
-        && git pull \
-        && git checkout 48143da \
-        && git submodule update --init --recursive \
-        && conda env create -f CondaEnvironment.yml \ 
-        && source activate GraphAligner \
-        && make bin/GraphAligner \
-        && cp bin/GraphAligner /usr/local/bin/GraphAligner \
-        && cd ../ \
-        && exit
-
 # Install the conda environment
 COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
@@ -93,4 +75,4 @@ RUN mkdir /scripts
 COPY scripts/beehave.R /scripts/beehave.R
 RUN chmod 777 /usr/local/bin/pgge && chmod 777 /scripts/beehave.R
 
-ENTRYPOINT [ "/bin/bash", "-l", "-c" ]
+ENTRYPOINT [ "/bin/sh", "-c", "-l" ]