work in progress
To run on windows, use powershell:
docker build -t ktel .; docker run -v //f//data://data ktel python get_srr.py SraRunTable.txt kmer_sample_min.txt --check_fasta true --fasta_limit 3000;
Make sure you mark the data directory drive as a shared drive from the docker manager app.
kmer_sample_min.txt contains:
- line 1 - the telomere k-mer
- lines 2-1319 - a random sample
- lines 1320 - 1583 - Tarmo's Alu-list
- lines 1584 - 3083 k-mers from telomere-length associated SNP-s (Variation-Locations-Homo_sapiens_Phenotype_Locations_Telomere_length.csv)
On mamba run with nohup ... &>/dev/null &
###Analysis
To run the analysis:
- build the docker image from /analysis dockerfile
docker run -d -p=6006:6006 -p=8888:8888 -v=//f//srv//notebooks://srv keras- navigate to localhost:8888 and open the notebook