diff --git a/.circleci/config.yml b/.circleci/config.yml index 9011fb10..0719f951 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -219,17 +219,3 @@ workflows: requires: - build - get_example_data - # - build-docker: - # requires: - # - build - # - getenvs - # - assembly_and_genecatalog - # filters: - # branches: - # only: master - # - publish-latest: - # requires: - # - build-docker - # filters: - # branches: - # only: master diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index a9d85c4e..00000000 --- a/Dockerfile +++ /dev/null @@ -1,89 +0,0 @@ -from continuumio/miniconda3 - - - -################## METADATA ###################### -LABEL base.image="continuumio/miniconda3" -LABEL version="$version" -LABEL software="metagenome-atlas" -LABEL software.version="2" -LABEL about.summary="Three commands to start analysing your metagenome data" -LABEL about.home="https://github.com/metagenome-atlas/atlas" -LABEL about.documentation="https://metagenome-atlas.rtfd.io" -LABEL license="BSD-3" -LABEL about.tags="metagenomics, annotation, snakemake, assembly, genomic-binning, functional-annotation, taxonomic-classifications" - -################## MAINTAINER ###################### -MAINTAINER Silas Kieser - -# Switch back to root for some install - -USER root -RUN export LC_ALL=en_US.UTF-8 -RUN export LANG=en_US.UTF-8 - -# setup miniconda -RUN conda config --add channels bioconda -RUN conda config --add channels conda-forge -RUN conda config --set always_yes true - -# download atlas -ENV version="2.3.beta2" -RUN wget https://github.com/metagenome-atlas/atlas/archive/${version}.tar.gz -RUN tar -xzf ${version}.tar.gz && mv atlas-${version} atlas -WORKDIR /atlas - - -#install metagenome atlas -RUN conda env update -n base --file atlasenv.yml -RUN python setup.py install - -# short test -RUN atlas --help -RUN atlas --version - -ENV databaseDir="/databases" -ENV WORKING_DIR='/.test/Dryrun' - -# Dryrun -RUN atlas init --db-dir $databaseDir --threads 3 -w $WORKING_DIR .test/reads/empty -RUN atlas run all -w $WORKING_DIR --dryrun - -# download conda packages -RUN atlas run all -w $WORKING_DIR --create-envs-only -RUN atlas run None "logs/checkm_init.txt" -w $WORKING_DIR - -# Download databases -# RUN atlas download --db-dir $databaseDir - -RUN chmod a+w $databaseDir - -# update atlas -RUN rm -rf atlas -RUN pip uninstall -y metagenome-atlas -RUN git clone https://github.com/metagenome-atlas/atlas.git -RUN cd atlas ; pip install . - -# short test -RUN atlas --help -RUN atlas --version - -# get example data -RUN git clone https://github.com/metagenome-atlas/example_data.git - - - -ENV WORKING_DIR='/AtlasTest' -# Dryrun -RUN atlas init --db-dir $databaseDir --threads 4 --interleaved-fastq -w $WORKING_DIR example_data/reads/test -RUN atlas run all -w $WORKING_DIR --dryrun -RUN atlas run all genomes/tree/checkm.nwk -w $WORKING_DIR --resources mem=50 java_mem=50 --omit-from download_gtdb add_eggNOG_header - -RUN atlas run all genomes/tree/checkm.nwk -w $WORKING_DIR --create-envs-only -RUN rm -r example_data -RUN chmod a+w $databaseDir $databaseDir/* - -RUN mkdir /WD -WORKDIR /WD - -CMD atlas diff --git a/docker.sh b/docker.sh deleted file mode 100644 index 2a528039..00000000 --- a/docker.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env bash - - -echo " -Your present working directory is mounted on /WD in the docker container. -The atlas databases are found on the docker in /databases. - -you can run atlas as folows: - - atlas init -db-dir /databases path/to/fastq/inside/your/workindirectory - -This should create a sample.tsv and a config.yaml. - -after that run: - - atlas run all - -" - -mkdir -p AtlasDB/GTDB-TK AtlasDB/EggNOGV2 -docker run -i -u $(id -u):$(id -g) -v $(pwd):/WD -v AtlasDB/EggNOGV2:/databases/EggNOGV2 -v AtlasDB/GTDB-TK:/databases/GTDB-TK -t metagenomeatlas/atlas:latest /bin/bash - - -# https://github.com/metagenome-atlas/example_data -# cd example_data -# docker.sh -# ls diff --git a/docs/usage/docker.rst b/docs/usage/docker.rst deleted file mode 100644 index 4051f846..00000000 --- a/docs/usage/docker.rst +++ /dev/null @@ -1,59 +0,0 @@ - - - -.. _setup_docker: - -Docker -****** - -We recommend to use the conda package as it allows deployment on clusters. -However, if you want to directly start using atlas on a small metagenome you can use the docker container:: - - docker pull metagenomeatlas/atlas - -Go to a directory on your filesystem where you have the fastq files in a subfolder, e.g. in ``reads`` -Your present working directory will be mounted on ``/WD`` in the docker container. - -The docker container contains all the dependencies and some of the databases in ``/databases`` . -The databases for functional and taxonomic annotation are downloaded while running. -To not loose the databases after exiting the docker we recommend to mount them also on your disk. - -Create:: - - mkdir -p AtlasDB/GTDB-TK AtlasDB/EggNOGV2 - -Then run the docker:: - - docker run -i -u $(id -u):$(id -g) -v $(pwd):/WD -v $(pwd)/AtlasDB/EggNOGV2/:/databases/EggNOGV2 -v $(pwd)/AtlasDB/GTDB-TK/:/databases/GTDB-TK -t metagenomeatlas/atlas:latest /bin/bash - -Inside the docker you can run atlas as folows:: - - atlas init -db-dir /databases /WD/reads - -This should create a sample.tsv and a config.yaml, whcih you can edit on your system. -Important don't forget to align the memory of your computer with the memory defined in the config file. - -after that run:: - - atlas run all - - -Test docker ------------ - -Testing atlas using the docker container works similarly to the above example. - -Create a working directory:: - - mkdir DockerTest; cd DockerTest - -get the example data:: - - git clone https://github.com/metagenome-atlas/example_data.git - -Set up the docker as explained :ref:`here ` and run it:: - - mkdir -p AtlasDB/GTDB-TK AtlasDB/EggNOGV2 - docker run -i -u $(id -u):$(id -g) -v $(pwd):/WD -v $(pwd)/AtlasDB/EggNOGV2/:/databases/EggNOGV2 -v $(pwd)/AtlasDB/GTDB-TK/:/databases/GTDB-TK -t metagenomeatlas/atlas:latest /bin/bash - -Inside the docker you have access to the ``example_data`` and you can initialize and run atlas test example as above.