A collection of scripts for managing the Harvard Odyssey cluster, including quantifying usage, identifying files that can be compressed, and more.
See the head of each script for a brief description and usage instructions.
All scripts are quite basic and can be improved in various ways, but they should be useful.
bed_compress -
calc_genomics_files_sizes - calculate the size of common, uncompressed genomics file formats (based on file extension) in a set of directories
calc_last_use - output a timestamp for the last manipulated file in a set of directories
calc_usage - calculate the amount of data storage of all files in a set of directories that counts against the lab quota
calc_usage.jobscript - calls the above calc_usage program in a formal Slurm job script
check_fairshare - summarize current cluster fairshare state for lab
check_job_parameters - summarizes the Slurm run parameters of queued or running jobs
check_storage_quota - summarize current cluster storge usage in the scratchlfs and holylfs locations
compressMaker - automated compression of raw MAKER outputs
compressRepMod - automated compression of raw RepeatModeler outputs
compressSupernova - automated compression of raw Supernova outputs
compressTrinity - automated compression of raw Trinity outputs
doc_template.md - template markdown file for creating documentation of programs or scripts
fastq_compress - Slurm job script for compressing all larger (>100 MB) FASTQ files in a directory using GZIP
gff_compress - Slurm job script for compressing all larger (>100 MB) GFF files in a directory using BGZIP/TABIX
intrun - start up an interactive session so commands are not run on login nodes
jobscript_template - write a job script template to the terminal for help creating a new job script
sam_compress - Slurm job script for compressing all larger (>100 MB) SAM files in a directory to BAM
switch_partition_all - switch the run partition of all queued jobs
switch_partition_single - switch the run partition of a single queued job
switch_time_all - change the time limit of all queued jobs
switch_time_single - change the time limit of a single queued job
vcf_compress - Slurm job script for compressing all larger (>100 MB) VCF files in a directory using BGZIP/TABIX