Add in get-apt installation for bedtools and samtools. Move away from…

… trying with Conda
milnus · Oct 14, 2021 · b32c2a6 · b32c2a6
1 parent 765538f
commit b32c2a6
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -7,8 +7,11 @@ RUN pip3 install .
 
 # Override some of the dependencies with the hard-coded versions
 RUN pip3 install -r requirements-dev.txt
-RUN conda install -c bioconda bedtools=2.29.9
-RUN conda install -c bioconda samtools=1.9
+
+RUN apt-get update && apt-get install -y \
+  bedtools=2.29.9 \
+  samtools=1.9 \
+  && rm -rf /var/lib/apt/lists/*
 #bedtools==2.29.2
  # TODO - add docker container with bedtools - biocontainers?
 #samtools==1.9
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,6 +1,5 @@
 # Dependencies, with versions explicitly declared for development and testing
 biopython==1.79
 pybedtools==0.8.2
-conda
 # Packages that are not dependencies but used for building or testing
 pylint