Utility scripts to work with Genologics Clarity LIMS
git clone https://github.com/UMCUGenetics/USEQ_tools.git
cd USEQ_tools
virtualenv env
. env/bin/activate
pip install -r requirements.txtCreate config.py file
BASEURI= USERNAME= PASSWORD=
MAIN_LOG=<LOG_FILE> MAIL_SENDER= MAIL_ADMINS=[
]
RAW_DIR = RUN_PROCESSES=['NextSeq Run (NextSeq) 1.0','USEQ - NextSeq Run', 'MiSeq Run (MiSeq) 4.0', 'USEQ - MiSeq Run','HiSeq Run (HiSeq) 5.0','USEQ - HiSeq Run'] ISOLATION_PROCESSES=['Qiagen genomic tip DNA isolation','QiaSymphony RNA isolation','USEQ - Isolation'] LIBPREP_PROCESSES=['Enrich DNA fragments (TruSeq Nano) 4.0','Enrich DNA fragments (TruSeq Stranded mRNA) 5.0','Enrich DNA fragments (TruSeq Stranded Total RNA) 5.0','USEQ - Enrich DNA fragments'] ANALYSIS_PROCESSES=['USEQ - Analysis']
#stats settings RUNTYPE_YIELDS={ "Version3" : 20000000, #MiSeq "Version2" : 12000000, #MiSeq "NextSeq Mid" : 120000000, #NextSeq "NextSeq High" : 350000000, #NextSeq "HiSeq rapid" : 250000000, #Hiseq }
#Nextcloud settings NEXTCLOUD_HOST = NEXTCLOUD_WEBDAV_ROOT = 'remote.php/webdav/' NEXTCLOUD_RAW_DIR = 'sequencing_runs/' NEXTCLOUD_USER = NEXTCLOUD_PW = NEXTCLOUD_STORAGE = 1073741824000 #in bytes NEXTCLOUD_MAX = 90 #percent
#ROUTING config STEP_URIS = { 'Truseq DNA nano' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3152', 'Truseq DNA amplicon' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3152', 'Truseq RNA stranded polyA' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3158', 'Truseq RNA stranded ribo-zero' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3165', 'Illumina NextSeq' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3174', 'Illumina MiSeq' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3177', 'Illumina NovaSeq' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3180', 'USEQ - Library Pooling' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3172', 'USEQ - Post Sequencing' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3183', 'USEQ - Pool QC' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3173', 'USEQ - Analysis' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3184', 'USEQ - Encrypt & Send' : 'https://usf-lims-test.op.umcutrecht.nl/api/v2/configuration/workflows/706/stages/3185'
}
STEP_NAMES = { 'ISOLATION' : ['USEQ - Isolation'], 'LIBPREP' : ['USEQ - Bioanalyzer QC DNA'], 'POOLING' : ['USEQ - Library Pooling'], 'POOL QC' : ['USEQ - Aggregate QC (Library Pooling)'], 'SEQUENCING' : ['USEQ - MiSeq Run','USEQ - NextSeq Run', 'USEQ - NovaSeq Run'], 'POST SEQUENCING' : ['USEQ - BCL to FastQ']
}
COST_DB = 'http://wgs11.op.umcutrecht.nl/useq/useq_getfinance.php?type=all&mode=json'
#RUN MANAGEMENT SETTINGS DATA_DIR_CONVERSION = DATA_DIR_HPC = ARCHIVE_DIR =
CONV_INTEROP = BCL2FASTQ_PATH= BCL2FASTQ_PROCESSING_THREADS=10 BCL2FASTQ_WRITING_THREADS=4