SUBDOCK DOCK3.8

how to use subdock

Subdock is a utility for running UCSF docking workloads across multiple platforms.

There are four essential ingredients that go in to every docking run-

1. ligand files (db2, set by INPUT_SOURCE)

2. receptor files (dockfiles, set by DOCKFILES)

3. dock executable (set by DOCKEXEC)

4. output destination (set by EXPORT_DEST)

Traditionally, arguments are specified to SUBDOCK via environment variables, e.g:

export INPUT_SOURCE=/some/path
export EXPORT_DEST=/some/path/2
...
bash subdock.bash

In the latest version of subdock, these arguments can be specified on the command line if desired, e.g:

bash subdock.bash --input-source=/some/path --export-dest=/some/path/2

Command line arguments will override environmental arguments. The name of a command line argument can be obtained by converting the environmental argument name into lowercase, switching '_' out with '-' & vice versa.

supported platforms

There are three platforms currently supported:

1. SLURM

2. SGE (Sun Grid Engine)

3. GNU Parallel (for local runs- ideal for testing)

One of these platforms must be specified- SLURM is the default. These platforms can be set by the

--use-slurm=true
--use-sge=true
--use-parallel=true

Arguments, respectively

supported file types

DOCK can be run on individual db2.gz files or db2.tgz tar packages.

The file type can be specified via the --use-db2=true or --use-db2-tgz=true arguments. db2.tgz is the default

Each job dispatched by SUBDOCK will consume BATCH_SIZE files, where BATCH_SIZE is equal to --use-db2-batch-size or --use-db2-tgz-batch-size depending on which file type is chosen.

The number of jobs dispatched by SUBDOCK is equal to ceil(N / BATCH_SIZE), where N is the total number of input files.

minimal examples

Using environmental arguments:

export INPUT_SOURCE=$PWD/sdi.txt
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles
export DOCKEXEC=$PWD/dock64
export USE_SLURM=true
bash subdock.bash

Using command line arguments:

bash subdock.bash --input-source=$PWD/sdi.txt --export-dest=$PWD/output --dockfiles=$PWD/dockfiles --dockexec=$PWD/dock64 --use-slurm=true

subdock help splash - all argument descriptions & defaults

SUBDOCK! Run docking workloads via job controller of your choice
=================required arguments=================
expected env arg: EXPORT_DEST, --export-dest
arg description: nfs output destination for OUTDOCK and test.mol2.gz files

expected env arg: INPUT_SOURCE, --input-source
arg description: nfs directory containing one or more .db2.tgz files OR a file containing a list of db2.tgz files

expected env arg: DOCKFILES, --dockfiles
arg description: nfs directory containing dock related files and INDOCK configuration for docking run

expected env arg: DOCKEXEC, --dockexec
arg description: nfs path to dock executable

=================job controller settings=================
optional env arg missing: USE_SLURM, --use-slurm
arg description: use slurm
defaulting to true

optional env arg missing: USE_SLURM_ARGS, --use-slurm-args
arg description: addtl arguments for SLURM sbatch command
defaulting to

optional env arg missing: USE_SGE, --use-sge
arg description: use sge
defaulting to false

optional env arg missing: USE_SGE_ARGS, --use-sge-args
arg description: addtl arguments for SGE qsub command
defaulting to

optional env arg missing: USE_PARALLEL, --use-parallel
arg description: use GNU parallel
defaulting to false

=================input settings=================
optional env arg missing: USE_DB2_TGZ, --use-db2-tgz
arg description: dock db2.tgz tar files
defaulting to true

optional env arg missing: USE_DB2_TGZ_BATCH_SIZE, --use-db2-tgz-batch-size
arg description: how many db2.tgz to evaluate per batch
defaulting to 1

optional env arg missing: USE_DB2, --use-db2
arg description: dock db2.gz individual files
defaulting to false

optional env arg missing: USE_DB2_BATCH_SIZE, --use-db2-batch-size
arg description: how many db2.gz to evaluate per batch
defaulting to 100

=================addtl job configuration=================
optional env arg missing: MAX_PARALLEL, --max-parallel
arg description: max jobs allowed to run in parallel
defaulting to -1

optional env arg missing: SHRTCACHE, --shrtcache
arg description: temporary local storage for job files
defaulting to /scratch

optional env arg missing: LONGCACHE, --longcache
arg description: longer term storage for files shared between jobs
defaulting to /scratch