BigRedButton.ini

[Paths]
#Where full/partial flowcell demultiplexing results are stored. Copies of parts of this are delivered to groups
baseData=/path/to/dissectBCL_results
# groupdata = /path if PI A and pi B have folders as /path/A/sequencing_data and /path/B/sequencing_data
groupData=/path/to/basedir/of/PI/folders
# where sequencing facility inspects QC reports
seqFacDir=/path/to/seqfacdir
# where the log-files show appear
logPath=/path/to/logdir

#Groups are stored under $groupData/groupName
groupData=/data
bioinfoCoreDir=/path/to/bioinfocoreDir

[Options]
#How long to sleep between runs, in hours, may be fractional
sleepTime=1
#valid library types, separate by a comma
validLibraryTypes=ChIP-Seq,stranded mRNA-Seq,stranded RNA-Seq,mRNA-Seq,RNA-Seq,WGS,ATAC-Seq
#Pipeline names, one for each of the aforementioned validLibraryTypes. Each pipeline is actually a function in the PushButton submodule
pipelines=DNA,RNA,RNA,RNA,RNA,DNA,ATAC
#valid organisms, separate by a comma
validOrganisms=human,mouse,drosophila
#An ordered list of the organism names used in the pipeline (the order matches validOrganisms)
organismNames=hg38,mm10,dm6
#Snakemake workflow base directory
snakemakeWorkflowBaseDir=/package/anaconda3/envs/snakePipes-1.0.0_alpha2/bin/RNA-seq
#Don't set these, they're just for passing info around
runID=

[Queue]
queueName=queue_name
parallelProcesses=10

[Parkour]
QueryURL=http://someserver.com/api/analysis_list/analysis_list/
ResultsURL=
user=foo@bar.com
password=supersecret
cert=path/to/cert.pem

[Email]
#Lists of recipients can be comma separated
errorTo=mustermann@ie-freiburg.mpg.de
finishedTo=mustermann@ie-freiburg.mpg.de
deepSeq=mustermann@ie-freiburg.mpg.de, another.example@ie-freiburg.mpg.de
fromAddress=some.user@ie-freiburg.mpg.de
host=localhost

[Galaxy]
URL=URL_to_galaxy_server
API key=the_api_key
verify=False
Users=path_to_user_file

[10x]
# separate pipelines specific for 10x Single Cell processing
RNA=/path/to/repo/10X_snakepipe/10x_scRNA/10x_scRNA
ATAC=/path/to/repo/10X_snakepipe/10x_scATAC/10x_scATAC


[external]
LibraryTypes =