Adds DIAMOND Docker image

diamond/2.x/BUILD.md

@@ -0,0 +1,11 @@
+# Building instructions
+
+Specify the diamond version in `diamond_version` and run:
+
+```bash
+diamond_version=2.1.8 && docker build ./ -t pegi3s/diamond:${diamond_version} --build-arg VERSION=${diamond_version}  && docker tag pegi3s/diamond:${diamond_version} pegi3s/diamond:latest
+```
+
+# Build log
+
+- 2.1.8 - 24/10/2023 - Hugo López Fernández

diamond/2.x/Dockerfile

@@ -0,0 +1,30 @@
+#
+#   Copyright 2018-2023 Hugo López-Fernández, Pedro M. Ferreira, Miguel 
+#   Reboiro-Jato, Cristina P. Vieira, and Jorge Vieira
+#
+#   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
+#
+#       http://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 debian:12.2-slim
+
+ARG VERSION
+
+RUN apt-get update && apt-get install -y wget
+
+RUN wget "https://github.com/bbuchfink/diamond/releases/download/v${VERSION}/diamond-linux64.tar.gz" -O /tmp/diamond.tar.gz && \
+	tar zxvf /tmp/diamond.tar.gz -C /usr/bin/ && rm /tmp/diamond.tar.gz
+
+RUN apt-get remove -y wget
+
+ENTRYPOINT ["diamond"]
+CMD ["help"]

diamond/2.x/README.md

@@ -0,0 +1,23 @@
+# This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)
+## (Please note that the original software licenses still apply)
+
+This image allows the usage of the [DIAMOND](https://github.com/bbuchfink/diamond) a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
+
+To list the main commands, simply run: `docker run --rm -it pegi3s/diamond`.
+
+To obtain the help of a specific command, you just need to run: `docker run --rm -it pegi3s/diamond <command>` (e.g. `docker run --rm -it pegi3s/diamond makedb`)
+
+# Using the DIAMOND image in Linux
+
+To run an application, you should adapt and run the following command: `docker run --rm -v /your/data/dir:/data pegi3s/diamond <command> <options>`
+
+In this command, you should replace:
+- `/your/data/dir` to point to the directory that contains the input files you want to analyze.
+- `<diamond>` to the name of the `DIAMOND` command you want to use.
+- `<options>` with the specific options of the `DIAMOND` application. These options will include the input/output files, which should be referenced under `/data/`.
+
+# Using the DIAMOND image in Windows
+
+Please note that data must be under the same drive than the Docker Toolbox installation (usually `C:`) and in a folder with write permissions (e.g. `C:/Users/User_name/`).
+
+As in the Linux case, to run an application, you should adapt and run the following command: `docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/diamond <command> <options>`

diamond/2.x/hooks/build

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+if [ -z ${VERSION} ]; then 
+    echo "VERSION environment variable not set."
+    exit 1
+else
+    echo "Building ${VERSION}"
+    docker build -f ${DOCKERFILE_PATH} --build-arg VERSION=${VERSION} -t ${IMAGE_NAME} .
+fi

docs/index.html

@@ -195,6 +195,9 @@ <h5>Programs:</h5>
               <li><a href="https://hub.docker.com/r/pegi3s/cutadapt/" target="_blank"><b>cutadapt</b></a> 
                 <a href="http://cutadapt.readthedocs.io/en/stable/guide.html" target="_blank">[doc]</a> - Sequence read trimming
               </li>
+              <li><a href="https://hub.docker.com/r/pegi3s/diamond/" target="_blank"><b>diamond</b></a> 
+                <a href="https://github.com/bbuchfink/diamond" target="_blank">[doc]</a> - Sequence alignment
+              </li>
               <li><a href="https://hub.docker.com/r/pegi3s/dnasp-v6" target="_blank"><b>dnasp-v6</b></a> 
                 <a href="http://www.ub.edu/dnasp/" target="_blank">[doc]</a> -  DNA sequence polymorphism
               </li>