Difference between revisions of "Linux"
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| Line 67: | Line 67: | ||
=== split input into chunks === | === split input into chunks === | ||
| + | <syntaxhighlight line='line'> | ||
channel.buffer(size:3) | channel.buffer(size:3) | ||
| + | </syntaxhighlight> | ||
| + | === group channel output into a single list === | ||
| + | |||
| + | |||
| + | <syntaxhighlight line='line'> | ||
| + | query = Channel.fromPath '*.fa' | ||
| + | species = Channel.from 'human', 'cow', 'horse' | ||
| + | |||
| + | process blast { | ||
| + | |||
| + | input: | ||
| + | val species | ||
| + | file query | ||
| + | |||
| + | output: | ||
| + | set val(species), file('result') into blastOuts | ||
| + | |||
| + | |||
| + | "blast -db nr -query $query" > result | ||
| + | |||
| + | } | ||
| + | </syntaxhighlight> | ||
Revision as of 20:29, 13 November 2018
user/groups
create group and add users to the group
1sudo groupadd metagenlab
2
3# a: append
4# G: group
5sudo usermod -a -G <group> <user>
- group file conf
1cat /etc/group
HDD
- liste des disques
1lsblk -io KNAME,TYPE,SIZE,MODEL
utilisation des diques
1df -h
Docker
- ubuntu network access problem
1sudo mv /etc/resolv.conf{,.bak}
2sudo ln -s /etc/resolv.conf /run/systemd/resolve/resolv.conf
Atom setup
NextFlow
Relauch killed jobs with increased ressources
process foo {
memory { 2.GB * task.attempt }
time { 1.hour * task.attempt }
errorStrategy { task.exitStatus == 140 ? 'retry' : 'terminate' }
maxRetries 3
script:
<your job here>
}split input into chunks
channel.buffer(size:3)group channel output into a single list
query = Channel.fromPath '*.fa'
species = Channel.from 'human', 'cow', 'horse'
process blast {
input:
val species
file query
output:
set val(species), file('result') into blastOuts
"blast -db nr -query $query" > result
}