Docker image

[Midnighter]

Hi @Ivarz,

I recently created a Docker image for conifer. I thought, I'd leave it here in case it's useful for you or someone else.

# Copyright (c) 2020, Moritz E. Beber.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

FROM bitnami/minideb:buster AS builder

RUN set -eux \
    && install_packages \
        build-essential \
        ca-certificates \
        git \
        libz-dev

WORKDIR /opt

RUN set -eux \
    && git clone https://github.com/Ivarz/Conifer.git \
    && cd Conifer \
    && git submodule update --init --recursive \
    && gcc -static -std=c99 -Wall -Wextra -O3 -D_POSIX_C_SOURCE=200809L -I third_party/uthash/src -I . src/utils.c src/kraken_stats.c src/kraken_taxo.c src/main.c -o conifer -l:libm.a -l:libz.a

FROM busybox:glibc

COPY --from=builder /opt/Conifer/conifer /

ENTRYPOINT ["/conifer"]

I'll track progress of this file over here.

[Ivarz]

Hi, @Midnighter, looks nice! I'll add link in README

[Midnighter]

I also put it on Docker hub. You can now pull the image directly from midnighter/conifer:latest without having to build the image locally. I also made some changes to the image that make it compatible with nextflow. (Requires bash and ps to be present.)

[Midnighter]

Just to note that I recently updated this to v1.0.2. Would be cool to auto deploy a new container when you release a new version. What do you think?