switch to ubuntu for docker tbprofiler

docker/Dockerfile.tbprofiler-0.9.8.1

@@ -1,11 +1,11 @@
-FROM mambaorg/micromamba:1.3.0 as app
+FROM ubuntu:focal
 
 #copy the reference genome to pre-compute our index
-COPY resources/tuberculosis.fasta /data/tuberculosis.fasta
+COPY tuberculosis.fasta /data/tuberculosis.fasta
 
-USER root
+#USER root
 WORKDIR /
-
+ENV TMPDIR="/data"
 ARG TBPROFILER_VER="6.2.1"
 
 # this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/
@@ -28,12 +28,14 @@ LABEL maintainer2.email="[email protected]"
 LABEL maintainer3="Tom Whalley"
 LABEL maintainer3.email="[email protected]"
 
-# Install dependencies via apt-get; cleanup apt garbage
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    wget \
-    ca-certificates \
-    procps && \
-    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y apt-utils wget bzip2 curl
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest| tar -xvj bin/micromamba \
+    && touch /root/.bashrc \
+    && ./bin/micromamba shell init -s bash -p /opt/conda  \
+    && grep -v '[ -z "\$PS1" ] && return' /root/.bashrc  > /opt/conda/bashrc   # this line has been modified \
+    && apt-get clean autoremove --yes \
+    && rm -rf /var/lib/{apt,dpkg,cache,log}
+
 
 # install tb-profiler via bioconda; install into 'base' conda env
 RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
@@ -45,7 +47,8 @@ RUN micromamba install --yes --name base --channel conda-forge jq
 RUN micromamba clean --all --yes
 
 # hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
-ENV PATH="/opt/conda/bin:${PATH}"
+ENV PATH="/root/micromamba/bin:${PATH}"
+
 
 # Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json
 # can also run 'tb-profiler list_db' to find the same version info