125 lines
4.4 KiB
Properties
125 lines
4.4 KiB
Properties
data.directory=data
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bin.directory=bin
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# Temporary files used by the analyses will be placed in directories here
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# (the text [UNIQUE], if present, will be replaced by a value unique to your running instance)
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temporary.file.directory.suffix=[UNIQUE]
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temporary.file.directory=temp/${temporary.file.directory.suffix}
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# Instructs I5 to completely clean up after a run
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delete.temporary.directory.on.completion=true
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# Perl and Python binaries to use
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perl.command=perl
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python3.command=python3
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# Binary file locations (required for setup.py)
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binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.3
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####################################
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# Member databases HMMs
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####################################
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antifam.hmm.path=${data.directory}/antifam/8.0/AntiFam.hmm
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gene3d.hmm.path=${data.directory}/gene3d/4.3.0/gene3d_main.hmm
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ncbifam.hmm.path=${data.directory}/ncbifam/19.0/ncbifam.hmm
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panther.hmm.path=${data.directory}/panther/19.0/famhmm/binHmm
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pfam-a.hmm.path=${data.directory}/pfam/38.2/pfam_a.hmm
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pirsf.sfhmm.path=${data.directory}/pirsf/3.10/sf_hmm_all
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pirsr.srhmm.path=${data.directory}/pirsr/2025_05/sr_hmm_all
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sfld.hmm.path=${data.directory}/sfld/4/sfld.hmm
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superfamily.hmm.path=${data.directory}/superfamily/1.75/hmmlib_1.75
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# A list of TCP ports that should not be used for messaging
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# (Apart from this, only ports > 1024 and < 65535 will be used)
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tcp.port.exclusion.list=3879,3878,3881,3882
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####################################
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# Precalculated match lookup service
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####################################
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# By default, if the sequence already has matches available from the EBI, this service will look them
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# up for you. Note: at present it will always return all the available matches, ignoring any -appl options
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# set on the command line
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precalculated.match.lookup.service.url=https://www.ebi.ac.uk/interpro/match-lookup
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precalculated.match.protein.lookup.batch.size=100
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precalculated.match.protein.insert.batch.size=500
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precalculated.match.protein.insert.batch.size.nolookup=4000
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# Proxy set up
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precalculated.match.lookup.service.proxy.host=
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precalculated.match.lookup.service.proxy.port=3128
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# Exclude sites from output (residue level annotations)
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exclude.sites.from.output=false
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####################################
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# Master/Standalone embedded workers
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####################################
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# Set the number of embedded workers to the number of processors that you would like to employ
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# on the machine you are using to run InterProScan.
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number.of.embedded.workers=6
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maxnumber.of.embedded.workers=8
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#################################
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# Distributed mode (Cluster mode)
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#################################
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# Grid name
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grid.name=lsf
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#grid.name=other-cluster
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# Project name for this run
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user.digest=i5GridRun
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# Grid jobs limit : number of jobs you are allowed to run on the cluster
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grid.jobs.limit=1000
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# Time between each bjobs/qstat command to check the status of jobs on the cluster
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grid.check.interval.seconds=120
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# Allow master interproscan to run binaries
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master.can.run.binaries=true
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# Deal with unknown step states
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recover.unknown.step.state=false
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# Grid submission commands (e.g. LSF bsub or SGE qsub) for starting remote workers
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# Commands the master uses to start new remote workers
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grid.master.submit.command=bsub -q QUEUE_NAME -M 8192
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grid.master.submit.high.memory.command=bsub -q QUEUE_NAME -M 8192
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# Commands a worker uses to start new remote workers
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grid.worker.submit.command=bsub -q QUEUE_NAME -M 8192
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grid.worker.submit.high.memory.command=bsub -q QUEUE_NAME -M 8192
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# Command to start a new worker (new jvm)
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worker.command=java -Xms2028M -Xmx9216M -jar interproscan-5.jar
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# This may be identical to the worker.command argument above, however you may choose to select
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# a machine with a much larger available memory, for use when a StepExecution fails.
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worker.high.memory.command=java -Xms2028M -Xmx9216M -jar interproscan-5.jar
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# Set the number of embedded workers to the number of processors that you would like to employ
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# on the node machine on which the worker will run.
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worker.number.of.embedded.workers=4
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worker.maxnumber.of.embedded.workers=4
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# Max number of connections to the master
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master.maxconsumers=48
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# Number of connections to the worker
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worker.maxconsumers=32
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# Throttled network?
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grid.throttle=true
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# Max number of jobs a tier 1 worker is allowed on its queue
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worker.maxunfinished.jobs=32
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# Network tier depth
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max.tier.depth=1
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# Active MQ JMS broker temporary data directory
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jms.broker.temp.directory=activemq-data/localhost/tmp_storage
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