Merge pull request #2 from stjudecab/fastcat

Add the fastcat tool

.github/workflows/build.yml

@@ -6,6 +6,7 @@ on:
       - 'deepmod2/**'
       - 'deepmod2-gpu/**'
       - 'annovar/**'
+      - 'fastcat/**'
     branches:
       - main
   pull_request:
@@ -24,6 +25,8 @@ jobs:
             platforms: linux/amd64
           - app: annovar
             platforms: linux/amd64,linux/arm64
+          - app: fastcat
+            platforms: linux/amd64,linux/arm64
 
     steps:
       - name: Checkout code

fastcat/Dockerfile

@@ -0,0 +1,42 @@
+FROM mambaorg/micromamba:2-ubuntu22.04 AS source
+
+USER $MAMBA_USER
+
+# set work directory
+WORKDIR /tmp
+
+# copy environment file
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+
+# create environment from yml file
+RUN micromamba env create -f environment.yml \
+  && micromamba clean --all --yes \
+  && rm /tmp/environment.yml
+
+FROM mambaorg/micromamba:2-ubuntu22.04 AS final
+
+ARG BUILD_VERSION=v0.18.6
+
+################## METADATA ######################
+LABEL base_image="micromamba:2-ubuntu22.04"
+LABEL version="1"
+LABEL software="fastcat"
+LABEL software.version="${BUILD_VERSION}"
+LABEL about.summary="Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences."
+LABEL about.home="https://github.com/epi2me-labs/fastcat"
+LABEL about.documentation="https://github.com/epi2me-labs/fastcat/blob/master/README.md"
+LABEL about.license_file="https://github.com/epi2me-labs/fastcat/blob/master/LICENSE"
+LABEL about.tags="Genomics"
+LABEL extra.identifiers.biotools="fastcat"
+
+COPY --from=source /opt/conda/envs/fastcat /opt/conda/envs/fastcat
+
+RUN echo "micromamba activate fastcat" >> ~/.bashrc
+
+WORKDIR /app
+
+# default command
+CMD ["fastcat", "--help"]
+
+# add mantainer
+MAINTAINER Haidong Yi <[email protected]>

fastcat/README.md

@@ -0,0 +1,67 @@
+# Fastcat Docker Image
+
+This Dockerfile builds a container for Fastcat, a tool that provides simple utilities to concatenate .fastq(.gz) files whilst creating a summary of the sequences.
+
+## Build
+
+To build the image:
+
+```bash
+docker build -t fastcat:v0.18.6 .
+```
+
+You can specify a different version using the `BUILD_VERSION` argument:
+
+```bash
+docker build --build-arg BUILD_VERSION={your_version} -t fastcat:{your_version} .
+```
+
+## Usage
+
+Run the container:
+
+```bash
+docker run --rm fastcat:v0.18.6 fastcat --help
+```
+
+This will display the help message for `Fastcat`. To run specific commands, replace `--help` with your desired arguments.
+
+## Features
+
+- Created based on `micromamba` image
+- Bundled with other useful utilities (e.g. `bzip2`, `split`, etc.)
+- Fastcat version: v0.18.6 (default, can be changed during build). For more versions, you can check it using `conda / mamba search`.
+
+## License
+
+Copyright (c) 2020-, Oxford Nanopore Technologies Plc. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* All advertising materials mentioning features or use of this software must
+  display the following acknowledgement: This product includes software
+  developed by Oxford Nanopore Technologies Plc.
+
+* Neither the name of Oxford Nanopore Technologies Plc. nor the names of
+  its contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY Oxford Nanopore Technologies Plc. AS IS AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL Oxford Nanopore Technologies Plc. BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

fastcat/environment.yml

@@ -0,0 +1,14 @@
+name: fastcat
+channels:
+    - nanoporetech
+    - conda-forge
+    - bioconda
+dependencies:
+    - python ==3.8.*
+    - ezcharts ==0.11.2
+    - pysam ==0.22.0
+    - fastcat ==0.18.6
+    - pandas <2.0.0
+    - epi2melabs ==0.0.53
+    - samtools ==1.19.2
+    - csvtk

fastcat/version

@@ -0,0 +1 @@
+v0.18.6