To test if you have installed HLA-MA correctly, you can run it on the provided test data.
If you did not already, activate the conda environment
# source activate hlama
and download HLA-MA from github for the test data.
# git clone https://github.com/bihealth/hlama.git
Then, call HLA-MA:
# cd hlama
# hlama --tumor-normal tests/data/tumor_normal/donors.tsv --work-dir TEST --reads-base-dir tests/data/tumor_normal --num-threads 4
Afterwards, you should find the following files and directories in TEST:
data.json
donor1_normal.d
donor1_tumor.d
donor1_tumor_rna.d
donor2_normal.d
donor2_tumor.d
report.txt
Snakefile
tmp
with the HLA-MA results in report.txt and all optitype results in the directories suffixed with .d.
# cat report.txt
donor2_tumor OK OK
donor1_tumor OK OK
donor1_tumor_rna OK 1