Linux

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

• atom - ipython - Hydrogen package

NextFlow

1. http://nextflow-io.github.io/patterns/index.html#_get_process_work_directory
2. https://github.com/sanger-pathogens/companion/blob/master/annot.nf#L658
3. https://nextflow-io.github.io/nf-hack18/training.html#_basic_language_structures_and_commands

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

}

In the above example a BLAST task is executed for each pair of species and query that are received. When the task completes a new tuple containing the value for species and the file result is sent to the blastOuts channel.

make SSH listen to alternative port (eg 3389 rdp)

• edit "/etc/ssh/sshd_config"
• add "Port 3389"

Bash error handling - exit code

Capture exit code in piped commands

set -o pipefail

Example: if grep cannot catch any match, it will return an exit code 1 (error) that will be catched if this option is set (default behaviour in snakemake rules)

fastaStat.py -f genome_fasta.fasta -l | grep contig_40 | sed 's//contig_/'

Print the error code

echo $?

If we do not whant the error to be catched, we can handle the exit code the following way:

fastaStat.py -f genome_fasta.fasta -l | grep contig_40 || true | sed 's//contig_/'

• see http://redsymbol.net/articles/unofficial-bash-strict-mode/