qdd-docker - QDD in a Docker
We foster the openness, integrity, and reproducibility of scientific research.
Scripts and funtion used deploy QDD version 3.1+ and all required tools (excluding RepeatMasker).
In microsatellite development, high throughput sequencing has replaced the classical cloning based methods and in this process the first two versions of QDD played an important role by dealing with the essential bio-informatics steps leading from raw sequences to primer design - Now in a Docker
QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate. Meglécz E1, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Grenier R, Martin JF. Mol Ecol Resour. 2014 Nov;14(6):1302-13.
This repository hosts both scripts and funtion used deploy QDD version 3.1+ and all required tools (excluding RepeatMasker).
To look at our scripts and raw results, browse through this repository. If you want to reproduce our results, you will need to clone this repository, build the docker, and the run all the scripts. If you want to use our data for our own research, fork this repository and cite the authors.
All required files and tools run in a self-contained docker image.
git clone https://github.com/pseudogene/qdd-docker.git
cd qdd-docker
If you plan to use the contamination check from a local copy of the NCBI nt database (-check_contamination 1), you need to get a copy it. Create a folder to store it and run the installation script
mkdir /blast
make -f Makefile.nt DEST=/blast
docker build --rm=true -t qdd .
To import and export the results of your analyse you need to link a folder to the docker. It this example your data will be store in qdd_test (current filesystem) which will be seem as been /qdd from within the docker by using -v <absolute_path_userfolder>/qdd_test:/qdd. Similarly the NCBI nt database stored in /blast (current filesystem) will be seem as been /blast_databases from within the docker.
docker run -i -t --rm \
-v <absolute_path_userfolder>/qdd_test:/qdd \
-v /blast:/blast_databases \
qdd /bin/bash
Make sure your input files are in a sub-folder in <absolute_path_userfolder>/qdd_test. Refer to QDD version 3.1+ manual for tutorials and examples.
To run the full pipeline:
QDD.pl -input_folder ./example -out_folder ./output -fastq 1 -check_contamination 1 -local_blast 0
If you have any problems with or questions about the scripts, please contact us through a GitHub issue. Any issue related to QDD itself must be done directly with the QDD authors from QDD website.
You are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can.
The content of this project itself including the raw data and work are licensed under the Creative Commons Attribution-ShareAlike 4.0 International License, and the source code presented is licensed under the GPLv3 license.