Replication Data for: New insights into adaptation and population structure of cork oak using genotyping by sequencing (docker image)

This dataset contains the docker image containing the anlyses environment (and software) used in the title study. Load it with the command: docker load --input q.suber_gbs_data_analyses.tar The container can then be started. In order to be able to access the results from your hosts system, the output directory should be mounted from the hosts system in the container with the following command: docker run -v /full/path/to/output/dir:/home/qsuber/Qsuber_data_analysis/Analyses -i -t stunts/q.suber_gbs_data_analyses:latest (or another tag of your choice) Make sure the Analyses directory is writable by the docker daemon (you will usually want to chmod 777 that directory). If you wish to use different input files (.vcf and .loci files) you may add another mount parameter afer the first: -v /full/path/to/input/dir:/home/qsuber/Qsuber_data_analysis/ipyrad_outfiles The input directory should contain the files: qsuber_clust95_lq3.loci and qsuber_clust95_lq3.vcf. If you want to user different filenames, you may do so, but don't forget to change them in the Makefile too. Also note that the Makefile is configured to use 4 threads by default. You may want to change that parameter depending on your case. You can then start the analysis by running: su qsuber cd ~/Qsuber_data_analysis make all Wait a few days (depending on your system, of course), and the data analysis should be ready. Once this step is finished, run: make blast to perform BLAST searches of "non-neutral" markers against the Q. lobata genome.