tb-profiler container

docker/Dockerfile.tbprofiler-0.9.8

@@ -1,12 +1,10 @@
-FROM mambaorg/micromamba:1.3.0
+FROM mambaorg/micromamba:1.3.0 as app
 
-LABEL maintainer="[email protected]" \
-about.summary="container for the tb-profiler"
+#copy the reference genome to pre-compute our index
+COPY resources/tuberculosis.fasta /data/tuberculosis.fasta
 
-COPY bin/ /opt/bin/
-COPY resources/tuberculosis.fasta ~/tuberculosis.fasta
-
-ENV PATH=/opt/bin:$PATH
+USER root
+WORKDIR /
 
 ARG TBPROFILER_VER="5.0.1"
 
@@ -15,6 +13,19 @@ ARG TBPROFILER_VER="5.0.1"
 # this was the latest commit as of 2023-10-26
 ARG TBDB_VER="e25540b"
 
+# LABEL instructions tag the image with metadata that might be important to the user
+LABEL base.image="micromamba:1.3.0"
+LABEL dockerfile.version="1"
+LABEL software="tbprofiler"
+LABEL software.version="${TBPROFILER_VER}"
+LABEL description="The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database."
+LABEL website="https://github.com/jodyphelan/TBProfiler/"
+LABEL license="https://github.com/jodyphelan/TBProfiler/blob/master/LICENSE"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="[email protected]"
+
 # Install dependencies via apt-get; cleanup apt garbage
 RUN apt-get update && apt-get install -y --no-install-recommends \
     wget \
@@ -26,13 +37,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
     tb-profiler=${TBPROFILER_VER} && \
     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}"
-
-# 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
-# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER}
-RUN tb-profiler update_tbdb --commit ${TBDB_VER}
 
 # hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
 ENV PATH="/opt/conda/bin:${PATH}"
@@ -42,5 +46,5 @@ ENV PATH="/opt/conda/bin:${PATH}"
 # In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER}
 RUN tb-profiler update_tbdb --commit ${TBDB_VER}
 
-#pre-add our TB reference
-RUN tb-profiler update_tbdb --match_ref ~/tuberculosis.fasta
+WORKDIR /data
+RUN tb-profiler update_tbdb --match_ref tuberculosis.fasta