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server.conf
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server.conf
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[ _ ]
# name of the _SFTP_ server, as used when fetching data files (i.e.: same name as in netrc file)
fileserver=bs-openbis04.ethz.ch
# port used by SFTP, in case of non standard (you can also use ~/.ssh/config for that)
srvport=2222
# address of the _Web_ server whose API we are calling
apiurl=https://openbis-dsu.ethz.ch/openbis/
# experiment name in OpenBIS
expname=/BSSE_STADLER_COVID/STADLER_COVID/COVID_V
# the type for which need to search the experiment thourgh
samtype=ILLUMINA_FLOW_LANE
# base dircetory
basedir=/links/shared/covid19-pangolin/backup
# sub-directory to hold the unsorted downloaded datasets
download=openbis-downloads
# sub-directory to hold the sorted samples set
sampleset=sampleset
# working sub-directory
working=working
# linking instead of copying ?
# --reflink for CoW filesystems (ZFS, BTRFS)
# --hardlink for most unix-like filesystems
link=--link
# extra suffix - e.g.: mismatches = one
suffix=_MM_1
# group on the storage (inside download and sampleset)
storgrp=bsse-covid19-pangolin@d.ethz.ch
# parallel copy jobs
parallel=8
# whereto push the sequences at the end
releasedir=/links/shared/covid19-pangolin/pangolin/consensus_data/batch/
# timeout before rsync considers the transfer failed in seconds
rsynctimeout=1800
# SSH connection timeout
contimeout=300
# IO timeout
iotimeout=300