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.