Bash unable to assign variable

Question

#!/usr/bin/env bash
#SBATCH --partition=standard
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --mem=100G
USEAGE="metascript.sh <wd> <wd1>"
source ~/anaconda2/etc/profile.d/conda.sh
conda activate assembly
wd=$1
wd1=$2
cd $wd
cd $wd1 
for f in SRR*/ ; do
  [[ -e $f ]] || continue
  SRR=${f::-1}
  cd ../..
  jdid=$(sbatch -J FirstQC_$SRR ./pipelines/preprocessingbowtietrinity/FirstFastqc.sh $wd $wd1 $SRR)
  #echo ${jdid[0]}|grep -o '[0-9]\+'
  jobid=${jdid[0]}
  jobid1=${jobid[0]}|grep -o '[0-9]\+'
  #echo $jobid1

Hi all just having issues with my bash scripting, so I can print the line ${jdid[0]}|grep -o '[0-9]+' however when I assign it to a variable it is unable to return anything.

Are you expecting to feed ${jobid[0] to grep and capture the output in jobid1? That's jobid1=$( echo "${jobid[0]}" | grep -o '[0-9]\+' ). — chepner
– chepner, Commented Jun 22, 2021 at 20:23
jdid is a string. There's no benefit in treating it like an array. — William Pursell
– William Pursell, Commented Jun 22, 2021 at 20:38

damienfrancois · Accepted Answer · 2021-06-22 20:40:29Z

1

If the idea is to extract just the job ID from the output of sbatch, you can also use sbatch's --parsable argument. See here in the documentation.

jdid=$(sbatch --parsable -J FirstQC_$SRR ./pipelines/preprocessingbowtietrinity/FirstFastqc.sh $wd $wd1 $SRR)

and jdij will only contain the job ID if the cluster is not part of a federation.

answered Jun 22, 2021 at 20:40

damienfrancois

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Armali · Accepted Answer · 2021-06-22 19:50:16Z

0

  jobid1=${jobid[0]}|grep -o '[0-9]\+'
I can print the line ${jdid[0]}|grep -o '[0-9]+' however when I assign it to a variable it is unable to return anything.

In order to assign the output of a pipeline to a variable or insert it into a command line for any other purpose, you have Command Substitution at hand:

  jobid1=`echo ${jobid[0]}|grep -o '[0-9]\+'`

Of course, with bash this is better written as:

  jobid1=`<<<${jobid[0]} grep -o '[0-9]\+'`

answered Jun 22, 2021 at 19:50

Armali

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3 Comments

chepner Over a year ago

With bash, you don't need grep at all. [[ ${jobid[0]} =~ ([0-9]+) ]]; jobid1=${BASH_REMATCH[1]}.

William Pursell Over a year ago

With any shell (written after about 1996), this is better written jobid=$( ... ). Backticks are dead.

Armali Over a year ago

You seem to confuse old-style with dead; the documentation does not confirm your death certificate.

CrazyTux · Accepted Answer · 2021-06-22 19:53:14Z

0

If the issue is printing the line ${jdid[0]}|grep -o '[0-9]+' as your question.
Just put the line in double quotation marks and it will work out.
Here is a little test i made:

jobid1="{jobid[0]}|grep -o '[0-9]\+'"
echo $jobid1

the out put is {jobid[0]}|grep -o '[0-9]\+'

answered Jun 22, 2021 at 19:53

CrazyTux

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