git clone https://github.com/shenwei356/easy_sbatch.git
mkdir -p ~/bin
cp easy_sbatch ~/bin/

$ cat ~/.easy_sbatch/default.slurm 
#!/bin/bash
#
#SBATCH --partition $partition
#SBATCH --job-name $name
#SBATCH --nodes=1
#SBATCH --cpus-per-task=$ncpus
#SBATCH --mem=$mem
#SBATCH --time=$walltime
#SBATCH --output=$output
#SBATCH --error=$error


cd $$SLURM_SUBMIT_DIR
# echo run on node: $$HOSTNAME >&2

$cmd

usage: easy_sbatch [-h] [-lp | -ls] [-J NAME] [-c NCPUS] [-m MEM] [-p PARTITION] [-w WALLTIME] [-t TEMPLATE]
                   [-O SCRIPT] [-o OUTPUT] [-e ERROR] [-v]
                   command [files ...]

easy_sbatch - Batch submitting Slurm jobs with script template

https://github.com/shenwei356/easy_sbatch 

Slurm script template:

  - Default template is ~/.easy_qsub/default.slurm .
  - You can also choose another one via the option -t/--template.
  - You can edit the value of an option, e.g., replace "$partition"
    with the default partition of your cluster. But note that the
    corresponding option from the command line will not take effect
    since no variable name is ready to replace.

Supported replacement strings in command:

  - "{}" for the full path of a input file.
  - "{/}" for dirname.
  - "{%}" for basename.
  - "{^suffix}" for clipping $suffix.
  - "{%^suffix}" for clipping $suffix from basename.

The generated Slurm scripts are saved in /tmp/easy_qsub-user/ by default,
unless the flag -O/--script is set. If jobs are submitted successfully,
the scripts will be moved to the current directory. If not, they will
be removed.

Examples:

  1. A simple command (no file or data given):
      $ easy_sbatch 'cat /etc/hostname'

      $ ls
        -rw-r--r-- 1 shenwei cqmu   0 Dec 27 21:50 easy_sbatch.15565347.err
        -rw-r--r-- 1 shenwei cqmu   9 Dec 27 21:50 easy_sbatch.15565347.out
        -rw------- 1 shenwei cqmu 314 Dec 27 21:50 easy_sbatch.15565347.slurm

  2. Handling multiple files and specifying a job name:
      $ easy_sbatch 'ls {}' *.fq.gz -J list

      $ ls
        -rw-r--r-- 1 shenwei cqmu   0 Dec 27 21:54 list.15565371-read_1.fq.gz.err
        -rw-r--r-- 1 shenwei cqmu  13 Dec 27 21:54 list.15565371-read_1.fq.gz.out
        -rw------- 1 shenwei cqmu 317 Dec 27 21:54 list.15565371-read_1.fq.gz.slurm
        -rw-r--r-- 1 shenwei cqmu   0 Dec 27 21:55 list.15565373-read_2.fq.gz.err
        -rw-r--r-- 1 shenwei cqmu  13 Dec 27 21:55 list.15565373-read_2.fq.gz.out
        -rw------- 1 shenwei cqmu 317 Dec 27 21:54 list.15565373-read_2.fq.gz.slurm
        -rw-r--r-- 1 shenwei cqmu   0 Dec 27 20:04 read_1.fq.gz
        -rw-r--r-- 1 shenwei cqmu   0 Dec 27 20:04 read_2.fq.gz

  3. From stdin:
      $ ls *.fq.gz | easy_sbatch 'echo {/} {%} {%^.fq.gz}'

  4. Processing paired-ends FASTQ files:
      $ ls read_1.fq.gz | easy_sbatch 'echo seqtk mergepe {} {^_1.fq.gz}_2.fq.gz' -J pe

      $ ls
        -rw-r--r-- 1 shenwei cqmu   0 Dec 27 21:56 pe.15565379-read_1.fq.gz.err
        -rw-r--r-- 1 shenwei cqmu  40 Dec 27 21:56 pe.15565379-read_1.fq.gz.out
        -rw------- 1 shenwei cqmu 340 Dec 27 21:56 pe.15565379-read_1.fq.gz.slurm

      $ cat pe.15565379-read_1.fq.gz.out
        seqtk mergepe read_1.fq.gz read_2.fq.gz

positional arguments:
  command               command to submit
  files                 input files

optional arguments:
  -h, --help            show this help message and exit
  -lp, --local_p        run commands locally, parallelly
  -ls, --local_s        run commands locally, serially
  -J NAME, --name NAME  job name (default: easy_sbatch)
  -c NCPUS, --ncpus NCPUS
                        number of cpus required per task (default: 24)
  -m MEM, --mem MEM     memory (default: 24gb)
  -p PARTITION, --partition PARTITION
                        partition requested (default: kshdnormal)
  -w WALLTIME, --walltime WALLTIME
                        walltime (default: 30-00:00:00)
  -t TEMPLATE, --template TEMPLATE
                        script template (default: /home/shenwei/.easy_sbatch/default.slurm
  -O SCRIPT, --script SCRIPT
                        output script file
  -o OUTPUT, --output OUTPUT
                        file for batch script's standard output (default: <name>.<jobID>.out])
  -e ERROR, --error ERROR
                        file for batch script's standard error (default: <name>.<jobID>.err])
  -v, --verbose         verbosely print information. -vv for just printing command not creating scripts and submitting jobs

https://github.com/shenwei356/easy_sbatch