all: chmod import_runqc import_read_counts copy_SomaticAndTreatment_diagnostic queue_SomaticAndTreatment_diagnostic

chmod:
	chmod -R 775 Unaligned

import_runqc:
	php /mnt/storage2/megSAP/pipeline/src/NGS/runqc_parser.php -name "#00001" -run_dir Unaligned/../ -force

import_read_counts:
	php /mnt/storage2/megSAP/pipeline/src/NGS/import_sample_read_counts.php -stats Unaligned/Stats/Stats.json -db NGSD_TEST 

copy_SomaticAndTreatment_diagnostic:
	mv Unaligned/SomaticAndTreatment/Sample_DX181280_01/ /mnt/storage2/projects/diagnostic/SomaticAndTreatment/
	mv Unaligned/SomaticAndTreatment/Sample_DX181277_01/ /mnt/storage2/projects/diagnostic/SomaticAndTreatment/
	mv Unaligned/SomaticAndTreatment/Sample_DX181278_01/ /mnt/storage2/projects/diagnostic/SomaticAndTreatment/
	mv Unaligned/SomaticAndTreatment/Sample_DX181279_01/ /mnt/storage2/projects/diagnostic/SomaticAndTreatment/

queue_SomaticAndTreatment_diagnostic:
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX181280_01 -args '-steps ma,db -somatic'
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX181277_01 -args '-steps ma,vc,cn,db -somatic'
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'somatic' -samples DX181280_01 DX181277_01 -info tumor normal
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX181278_01 -args '-steps ma,db -somatic'
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'somatic' -samples DX181278_01 DX181277_01 -info tumor normal
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX181279_01 -args '-steps ma,db -somatic'
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'somatic' -samples DX181279_01 -info tumor
