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To save time avoiding typing long commands again and again, you can add aliases to your .bashrc
file (change only the aliases, unless you know what you’re doing).
[username@clust-slurm-client ]$ cat ~/.bashrc
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=
# User specific aliases and functions
alias qq="squeue -u username"
alias sa="sacct --format=JobID,JobName,Start,CPUTime,MaxRSS,ReqMeM,State"
alias ll="ls -lht --color=always"
It will work next time you connect to the server. When you type sa
, you will get the command sacct --format=JobID,JobName,Start,CPUTime,MaxRSS,ReqMeM,State
running.
It is possible to quickly rename all your samples using mv
. For instance if your samples are not named according to our workflow requirement sample_R1.fastq.gz
and sample_R2.fastq.gz
but sample.1.fastq.gz
and sample.2.fastq.gz
(dots instead of underscores and without R
) :
[username@clust-slurm-client Raw_fastq]$ ls
D192T27.1.fastq.gz
D192T27.2.fastq.gz
D192T28.1.fastq.gz
D192T28.2.fastq.gz
D192T29.1.fastq.gz
D192T29.2.fastq.gz
D192T30.1.fastq.gz
D192T30.2.fastq.gz
D192T31.1.fastq.gz
D192T31.2.fastq.gz
D192T32.1.fastq.gz
D192T32.2.fastq.gz
You can modify them using mv
and a loop on sample numbers.
[username@clust-slurm-client Raw_fastq]$ for i in `seq 27 32`; do mv D192T$i\.1.fastq.gz D192T$i\_R1.fastq.gz; done
[username@clust-slurm-client Raw_fastq]$ for i in `seq 27 32`; do mv D192T$i\.2.fastq.gz D192T$i\_R2.fastq.gz; done
Now sample names are OK:
[username@clust-slurm-client Raw_fastq]$ ls
D192T27_R1.fastq.gz
D192T27_R2.fastq.gz
D192T28_R1.fastq.gz
D192T28_R2.fastq.gz
D192T29_R1.fastq.gz
D192T29_R2.fastq.gz
D192T30_R1.fastq.gz
D192T30_R2.fastq.gz
D192T31_R1.fastq.gz
D192T31_R2.fastq.gz
D192T32_R1.fastq.gz
D192T32_R2.fastq.gz
BiBs
2023 parisepigenetics
https://github.com/parisepigenetics/bibs |
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s |
focus search bar ( enter to select, ▲ / ▼ to change selection) |
g c |
go to cluster |
g e |
go to edctools |
g f |
go to facility |
g g |
go to guidelines |
h |
toggle this help ( esc also exits) |