From dba535e27b4dad84ac3c892885b245bfadea2656 Mon Sep 17 00:00:00 2001 From: Michal Ziemski Date: Fri, 2 Jun 2023 15:42:24 +0200 Subject: [PATCH 1/2] VER: 2023.7.0.dev0 From 4943f8379b19fe64f482b3ee9f86762d262a9b18 Mon Sep 17 00:00:00 2001 From: Lina Kim Date: Tue, 28 Nov 2023 10:04:52 +0100 Subject: [PATCH 2/2] ENH: Add minimal Docker image for q2-fondue (#158) * Created Docker image and updated README * Update README.md Co-authored-by: Anja Adamov <57316423+adamovanja@users.noreply.github.com> * Incorporated suggestions for ncbi-tools * DOC: Directions for users to check Docker image works * Remove unnecessary refs to vdb-config and update README for optional configuration * Remove vdb-config shortcut and incorporate a committed container * Removed unnecessary apt-get commands --------- Co-authored-by: Anja Adamov <57316423+adamovanja@users.noreply.github.com> --- Dockerfile | 11 +++++++++++ README.md | 20 +++++++++++++++++++- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..cc49c7f --- /dev/null +++ b/Dockerfile @@ -0,0 +1,11 @@ +FROM mambaorg/micromamba +ARG MAMBA_DOCKERFILE_ACTIVATE=1 +RUN micromamba install -y -c https://packages.qiime2.org/qiime2/2023.2/tested/ \ + -c conda-forge -c bioconda -c defaults \ + q2cli q2-fondue +ENV PATH /opt/conda/bin:$PATH + +RUN mkdir $HOME/.ncbi +RUN printf '/LIBS/GUID = "%s"\n' `uuidgen` > $HOME/.ncbi/user-settings.mkfg + +CMD [ "/bin/bash" ] diff --git a/README.md b/README.md index 3998887..e6d727f 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@


## Installation -You can install q2-fondue using mamba in a conda environment of its own (option 1) or in an existing QIIME 2 environment (option 2) by following the steps described below. The current q2-fondue version supports QIIME 2 **v2021.4** or higher. +You can install q2-fondue using mamba in a conda environment of its own (option 1) or in an existing QIIME 2 environment (option 2) by following the steps described below. The current q2-fondue version supports QIIME 2 **v2021.4** or higher. Alternatively, a minimal Docker image is available to run q2-fondue methods (option 3 below). For both options 1 and 2 make sure to start by installing [mamba](https://mamba.readthedocs.io/en/latest/index.html) in your base environment: ```shell @@ -61,6 +61,24 @@ vdb-config -i vdb-config --proxy --proxy-disable no ``` +### Option 3: Use fondue via a public Docker image +Use containerization to integrate q2-fondue into your pipelines, or simply run reproducibly without the need for heavyweight package managers. [Read more about Docker here.](https://www.docker.com/get-started/) + +* Install [Docker](https://docs.docker.com/engine/install/) with the linked instructions +* Pull the [q2-fondue Docker image](https://hub.docker.com/layers/linathekim/q2-fondue/2023.2/images/sha256-214d0575eb4eaf435c5c4a7d29edf0fc082e47999b884b52a173f2ec469975f2?context=repo): +```shell +docker pull linathekim/q2-fondue:2023.2 +``` +* Within the container, refresh the QIIME 2 CLI cache to see that everything worked: +```shell +qiime dev refresh-cache +qiime fondue --help +``` +* If you need to configure a proxy server, run the following command: +```shell +vdb-config --proxy --proxy-disable no +``` + ## Space requirements Running q2-fondue requires space in the temporary (`TMPDIR`) and output directory. The space requirements for the output directory can be estimated by inserting the run or project IDs in the [SRA Run Selector](https://www.ncbi.nlm.nih.gov/Traces/study/). To estimate the space requirements for the temporary directory, multiply the output directory space requirement by a factor of 10. The current implementation of q2-fondue requires you to have a minimum of 2 GB of available space in your temporary directory.