run-all-rpbp-instances#

Call Rp-Bp for each sample in the configuration file.

usage: run-all-rpbp-instances [-h] [--profiles-only] [--merge-replicates]
                              [--run-replicates] [--write-unfiltered] [-k]
                              [--overwrite] [--tmp TMP]
                              [--flexbar-options [FLEXBAR_OPTIONS ...]]
                              [--star-executable STAR_EXECUTABLE]
                              [--star-options [STAR_OPTIONS ...]]
                              [--num-cpus NUM_CPUS] [--mem MEM] [--time TIME]
                              [--partitions PARTITIONS] [--no-output]
                              [--no-error] [--stdout-file STDOUT_FILE]
                              [--stderr-file STDERR_FILE] [--do-not-call]
                              [--use-slurm]
                              [--mail-type [{NONE,BEGIN,END,FAIL,REQUEUE,ALL,STAGE_OUT,TIME_LIMIT,TIME_LIMIT_90,TIME_LIMIT_80,TIME_LIMIT_50,ARRAY_TASKS} ...]]
                              [--mail-user MAIL_USER] [--log-file LOG_FILE]
                              [--enable-ext-logging] [--log-stdout]
                              [--no-log-stderr]
                              [--logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                              [--file-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                              [--stdout-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                              [--stderr-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                              config

Positional Arguments#

config: A YAML configuration file.

Named Arguments#

--profiles-only

Run the periodicity estimation only (ORF profile construction) for each sample in the configuration file.

Default: False

--merge-replicates

Predict Ribo-seq ORFs in merged profiles. If --merge-replicates, then use --run-replicates to also predict Ribo-seq ORFs in all samples.

Default: False

--run-replicates

With --merge-replicates, predict Ribo-seq ORFs in all samples and in merged profiles. This has no effect without --merge-replicates, i.e. predictions are made for all samples by default.

Default: False

--write-unfiltered

In addition to the default filtered predictions, output all overlapping predicted Ribo-seq ORFs.

Default: False

-k, --keep-intermediate-files

Keep all intermediate files. Intermediate files are necessary to perform read filtering quality control.

Default: False

--overwrite

Overwrite existing output.

Default: False

--tmp

A temporary directory (STAR).

Flexbar options#

--flexbar-options: A space-delimited list of options to pass to Flexbar. Each option is quoted separately as in "--flexbarOption value", using soft quotes, where flexbarOption is the long parameter name from Flexbar, and value is the value given to this parameter. If specified, Flexbar options will override default settings.

STAR options#

--star-executable

The name of the STAR executable

Default: “STAR”

--star-options

A space-delimited list of options to pass to STAR. Each option is quoted separately as in "--starOption value", using soft quotes, where starOption is the long parameter name from STAR, and value is the value given to this parameter. If specified, STAR options will override default settings.

slurm options#

--num-cpus

The number of CPUs to use (not only for SLURM). For STAR, --num-cpus are threads, but in general, this is number of processes to spawn. This value should not be greater than the number of cores available. When used with SLURM, this is equivalent to: --ntasks 1 --cpus-per-task <num-cpus>.

Default: 1

--mem

Real memory required (per node), mostly for STAR genome indexing (not only for SLURM). When used with SLURM, this is equivalent to: --mem=<mem>.

Default: “2G”

--time

Set a limit on the total run time of the job allocation. This is equivalent to: --time <time>.

--partitions

Request a partition for the resource allocation. This is equivalent to: -p <partitions>.

--no-output

Redirect stdout to /dev/null. This is equivalent to: --output=/dev/null. By default, stdout is redirected to --output=slurm-*.out.

Default: False

--no-error

Redirect stderr to /dev/null. This is equivalent to: --output=/dev/null. By default, stderr is redirected to --output=slurm-*.err.

Default: False

--stdout-file

Log file (stdout) if not --no-output. This is equivalent to: --output=stdout-file.

--stderr-file

Log file (stderr) if not --no-error. This is equivalent to: --output=stderr-file.

--do-not-call

Do not execute the program (dry run).

Default: False

--use-slurm

Submitted calls to SLURM.

Default: False

--mail-type

Possible choices: NONE, BEGIN, END, FAIL, REQUEUE, ALL, STAGE_OUT, TIME_LIMIT, TIME_LIMIT_90, TIME_LIMIT_80, TIME_LIMIT_50, ARRAY_TASKS

Notify user by email when certain event types occur, if --mail-user is specified.

Default: [‘FAIL’, ‘TIME_LIMIT’]

--mail-user

User to receive email notification of state changes as defined by --mail-type.

logging options#

--log-file

Log file (logging is redirected to this file, in addition to stdout and stderr, if specified).

Default: “”

--enable-ext-logging

Enable logging for external programs that may be disabled by default, e.g. CmdStanPy.

Default: False

--log-stdout

Log to stdout (in addition to a file and stderr, if specified).

Default: False

--no-log-stderr

Do not send logging to stderr.

Default: False

--logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for all logs.

Default: “WARNING”

--file-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for the log file. This option overrides --logging-level.

Default: “NOTSET”

--stdout-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for stdout. This option overrides --logging-level.

Default: “NOTSET”

--stderr-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for stderr. This option overrides --logging-level.

Default: “NOTSET”