sbatchtools is a suite of shell scripts to automate slurm submissions
sruni automates the submission of creating and activating an interactive node
------------------------------ SRUN INTERACTIVE HELP ------------------------------
---------- PROGRAM == sruni (srun interactive)
---------- VERSION == 1.0.0
---------- DATE == 2023_04_20
---------- CONTACT == kew24 (template from [email protected] -- big thank you!)
---------- DISCRIPTION == automates creation of slurm interactive job
---------- PATH == export PATH=\$PATH:/path/to/sruni/directory
-------------------- COMMANDS --------------------
---------- USAGE == sruni [options]*
---------- FLAGS
[ -d | --debug ] == creates job script but does not execute
[ -h | --help ] == help function
---------- OPTIONS
[ -c | --cores <int> ] == number of cores per job 1 to 80, default 1 core
[ -N | --name <name> ] == name specific to job, default STDIN
[ -p | --partition <name> ] == specify partition name, default any partition
[ -w | --walltime <int> ] == number of hours per job 1 to 336, default 24 hours
-------------------- EXAMPLES --------------------
sruni
sruni -c 4 -p short
------------------------------ SRUN INTERACTIVE HELP ---------------------------
sbatchs automates the submission of creating and activating of job submissions. sbatchs will automate single and array based submissions as well as linux and R based submissions.
------------------------------ SBATCH SUBMITTER HELP ------------------------------
---------- PROGRAM == sbatchs (sbatch submitter)
---------- VERSION == 1.0.0
---------- DATE == 2023_04_20
---------- CONTACT == kew24 (template from [email protected] -- big thank you!)
---------- DISCRIPTION == automates creation and submition of slurm sbatch scripts
---------- PATH == export PATH=\$PATH:/path/to/sbatchs/directory
-------------------- COMMANDS --------------------
---------- USAGE == sbatchs [options]* -s "command"
---------- FLAGS
[ -d | --debug ] == creates job script but does not execute
[ -h | --help ] == help function
---------- OPTIONS
[ -a | --array <file> ] == file containing column of sample names for array,
use SAMPLE as variable for sample name in command or script
[ -c | --cores <int> ] == number of cores per job 1 to 80, default 1 core
[ -n | --name <name> ] == name specific to job, default user name and date
[ -p | --partition <name> ] == specify partition name, default any partition
[ -r | --rscript <"command"> or <file> ] == command enclosed in double quotes or script file
[ -s | --script <"command"> or <file> ] == command enclosed in double quotes or script file
[ --script_args <args> ] == positional arguments passed to your bash script file
[ -w | --walltime <int> ] == number of hours per job 1 to 336, default 24 hours
-------------------- MULTIPLE COMMANDS --------------------
---------- USAGE == containg multiple compands with double quotes,
with each command on seperate line, see example
---------- COMMAND VARIABLES == must start with a backslash \$1
-------------------- EXAMPLES --------------------
touch sample_data.txt
sbatchs -n gzip_file -s "gzip sample_data.txt"
touch sample1_data.txt
touch sample2_data.txt
echo sample1 > sample_names
echo sample2 >> sample_names
sbatchs -n zip_comand -a sample_names -s "zip SAMPLE_data.zip SAMPLE_data.txt"
echo "zip SAMPLE_data.zip SAMPLE_data.txt" > sample_script
sbatchs -n zip_script -a sample_names -s sample_script -d
------------------------------ SBATCH SUBMITTER HELP ---------------------------