From 1c9c07d903733b5f3d9e56466e284163c4c4cd66 Mon Sep 17 00:00:00 2001
From: Tom Whalley <whalleyt@cardiff.ac.uk>
Date: Wed, 4 Sep 2024 16:08:13 +0000
Subject: [PATCH] mamba install

---
 docker/Dockerfile.ntmprofiler-0.9.9 | 76 +++++++++++++++++------------
 1 file changed, 44 insertions(+), 32 deletions(-)

diff --git a/docker/Dockerfile.ntmprofiler-0.9.9 b/docker/Dockerfile.ntmprofiler-0.9.9
index cbbf621..1c1382e 100644
--- a/docker/Dockerfile.ntmprofiler-0.9.9
+++ b/docker/Dockerfile.ntmprofiler-0.9.9
@@ -1,34 +1,46 @@
 FROM ubuntu:jammy
 
-ENV pathogenprofiler_version="3b4c6e2ffba8f7a44d12cc2ed4369ee635464093"
-ENV ntmprofiler_version="2e4116bff2c09461b2d452f4075c6589e0a66965"
-ENV ntmdb_version="93c979b4c3825c591e5bceb55f86538e10d556d2"
-
-ARG PATHOGEN_PROFILER_VERSION="3b4c6e2ffba8f7a44d12cc2ed4369ee635464093"
-ARG NTM_PROFILER_VERSION="2e4116bff2c09461b2d452f4075c6589e0a66965"
-ARG NTMDB_VERSION="93c979b4c3825c591e5bceb55f86538e10d556d2"
-
-#python packages
-ENV PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq" \
-	PYTHON="python3.12 python3-pip python3-dev python3-packaging"
-
-#apt-get python stuff
-RUN apt-get update  && \
-	DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install \
-	tzdata software-properties-common && \
-	add-apt-repository ppa:deadsnakes/ppa && \
- 	apt install -y $PACKAGES $PYTHON && \
-	apt remove -y python3.8 && \
-	apt install -y python3.12-distutils python3.12-venv
-
-#reinstall pip
-RUN python3.12 -m ensurepip --upgrade
-RUN python3.12 -m pip install --upgrade setuptools
-
-#use pip to install ntm stuff
-RUN python3.12 -m pip install pysam joblib tqdm pydantic jinja2 rich-argparse packaging==24.1 
-RUN python3.12 -m pip install git+https://github.com/jodyphelan/pathogen-profiler.git@${PATHOGEN_PROFILER_VERSION}
-RUN python3.12 -m pip install git+https://github.com/jodyphelan/ntm-profiler.git@${NTM_PROFILER_VERSION}
-
-#update DB to our commit
-RUN ntm-profiler update_db --commit ${NTMDB_VERSION} 
+ENV ntmdb_version=93c979b4c3825c591e5bceb55f86538e10d556d2 \
+    ntmprofiler_version=0.4.0 \
+    TMPDIR="." 
+
+#USER root
+WORKDIR /
+ARG NTMPROFILER_VER="0.4.0"
+ARG NTMDB_VER="93c979b4c3825c591e5bceb55f86538e10d556d2"
+
+# this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/
+# commits are found on https://github.com/jodyphelan/tbdb/commits/master
+# this was the latest commit as of 2024-05-21
+ARG TBDB_VER="a5e1d48"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="0.9.9"
+LABEL software="tbprofiler"
+LABEL software.version="${NTMROFILER_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 maintainer3="Tom Whalley"
+LABEL maintainer3.email="twhalley93@gmail.com"
+
+#set env for root prefix
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+
+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  \
+    ntm-profiler=${NTMPROFILER_VER}
+
+# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
+ENV PATH="/opt/conda/bin:${PATH}"
+
+RUN tb-profiler update_tbdb --match_ref /data/tuberculosis.fasta --commit ${NTMDB_VER}
+