Help on Available functions¶

check_args¶

checks all the arguments in the parent frame. None of them should be null.

Description¶

This function may be optionally moved to a more generic package.

Usage¶

check_args(ignore, select)

Arguments¶

ignore: optionally ignore a few variables for checking.
select: optionally only check a few variables of the function.

Examples¶

Aliases: check_args .. Keywords:

check¶

Check consistency of flowdef and flowmat

Description¶

Currently checks S3 flowdef & flowmat for consistency.

Usage¶

check(x, ...)

## method for class 'flowmat'
check(x, ...)

## method for class 'flowdef'
check(x, verbose = get_opts("verbose"), ...)

Arguments¶

x: a flowdef or flowmat object

...: suppled to check.classname function
verbose: be chatty

Examples¶

Aliases: check check.flowdef check.flowmat .. Keywords:

fetch¶

A generic functions to search for files

Description¶

These functions help in searching for specific files in the user’s space.

fetch_pipes(): Fetches pipelines in the following places, - - available in ‘pipelines’ folders in flowr and ngsflows packages. - - ~/flowr/pipelines - - github repos (currently not supported)

fetch_conf(): Fetches configuration files in the following places,

- available in ‘conf’ folders in flowr and ngsflows packages.
- ~/flowr/conf folder

By default flowr loads, ~/flowr/conf/flowr.conf and ~/flowr/conf/ngsflows.conf

Usage¶

fetch(x, places, urls, verbose = get_opts("verbose"))

fetch_pipes(x, places, last_only = FALSE, urls = get_opts("flowr_pipe_urls"), silent = FALSE, ask = TRUE)

fetch_conf(x = "flowr.conf", places, ...)

Arguments¶

x: name of the file to search for
places: places (paths) to look for it. Its best to use the defaults
urls: urls to look for, works well for pipelines.
verbose: be chatty?
last_only: [fetch_pipes only]. If multiple pipelines match the pattern, return the last one.
silent: [fetch_pipes() only]. logical, be silent even if no such pipeline is available.
ask: ask before downloading or copying, not used !

...: not used

Examples¶

{
fetch_conf("torque.sh")
}
[1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library/flowr/conf/torque.sh"

Aliases: fetch fetch_conf fetch_pipes .. Keywords:

flow¶

Flow constructor

Description¶

Flow constructor

Usage¶

flow(jobs = list(new("job")), name = "newflow", desc = "my_super_flow", mode = c("scheduler", "trigger", "R"), flow_run_path = get_opts("flow_run_path"), trigger_path = "", flow_path = "", version = "0.0", status = "", execute = "")

is.flow(x)

Arguments¶

jobs: list A list of jobs to be included in this flow
name: character Name of the flow. Defaults to 'newname'

Used in submit_flow to name the working directories.

desc: character Description of the flow

This is used to name folders (when submitting jobs, see submit_flow). It is good practice to avoid spaces and other special characters. An underscore ‘_’ seems like a good word separator. Defaults to ‘my_super_flow’. We usually use this to put sample names of the data.

mode: character Mode of submission of the flow.
flow_run_path: The base path of all the flows you would submit.

Defaults to ~/flows. Best practice to ignore it.

trigger_path: character

Defaults to ~/flows/trigger. Best practice to ignore it.

flow_path: character
version: version of flowr used to create and execute this flow.
status: character Not used at this time
execute: executtion status of flow object.

Examples¶

cmds = rep("sleep 5", 10)
qobj <- queue(platform='torque')
## run the 10 commands in parallel
jobj1 <- job(q_obj=qobj, cmd = cmds, submission_type = "scatter", name = "job1")

## run the 10 commands sequentially, but WAIT for the previous job to complete
## Many-To-One
jobj2 <- job(q_obj=qobj, cmd = cmds, submission_type = "serial",
 dependency_type = "gather", previous_job = "job1", name = "job2")

## As soon as first job on 'job1' is complete
## One-To-One
jobj3 <- job(q_obj=qobj, cmd = cmds, submission_type = "scatter",
 dependency_type = "serial", previous_job = "job1", name = "job3")

fobj <- flow(jobs = list(jobj1, jobj2, jobj3))

## plot the flow
plot_flow(fobj)
## **Not run**:
# ## dry run, only create the structure without submitting jobs
# submit_flow(fobj)
#
# ## execute the jobs: ONLY works on computing cluster, would fail otherwise
# submit_flow(fobj, execute = TRUE)
# ## **End(Not run)**

Aliases: flow is.flow .. Keywords:

get_unique_id¶

get_unique_id

Description¶

get_unique_id

Usage¶

get_unique_id(prefix = "id", suffix = "", random_length = 8)

Arguments¶

prefix: Default id. Character string to be added in the front.
suffix: Default ‘’. Character string to be added in the end.
random_length: Integer, defaults to 8. In our opinion 8 serves well, providing ‘uniqueness’ and not being much of a eyesore.

Examples¶

## **Not run**:
# get_unique_id(base = id, random_length = 8)## **End(Not run)**

Aliases: get_unique_id .. Keywords:

internal .. Author:

get_wds¶

Get all the (sub)directories in a folder

Description¶

Get all the (sub)directories in a folder

Usage¶

get_wds(x)

Arguments¶

x: path to a folder

Examples¶

Aliases: get_wds .. Keywords:

job¶

job class

Description¶

job class

Usage¶

job(cmds = "", name = "myjob", q_obj = new("queue"), previous_job = "", cpu = 1, memory, walltime, submission_type = c("scatter", "serial"), dependency_type = c("none", "gather", "serial", "burst"), ...)

Arguments¶

cmds: the commands to run
name: name of the job
q_obj: queue object
previous_job: character vector of previous job. If this is the first job, one can leave this empty, NA, NULL, ‘.’, or ‘’. In future this could specify multiple previous jobs.
cpu: no of cpu’s reserved
memory: The amount of memory reserved. Units depend on the platform used to process jobs
walltime: The amount of time reserved for this job. Format is unique to a platform. Typically it looks like 12:00 (12 hours reserved, say in LSF), in Torque etc. we often see measuring in seconds: 12:00:00
submission_type: submission type: A character with values: scatter, serial. Scatter means all the ‘cmds’ would be run in parallel as seperate jobs. Serial, they would combined into a single job and run one-by-one.
dependency_type: depedency type. One of none, gather, serial, burst. If previous_job is specified, then this would not be ‘none’. [Required]

...: other passed onto object creation. Example: memory, walltime, cpu

Examples¶

qobj <- queue(platform="torque")

## torque job with 1 CPU running command 'sleep 2'
jobj <- job(q_obj=qobj, cmd = "sleep 2", cpu=1)

## multiple commands
cmds = rep("sleep 5", 10)

## run the 10 commands in parallel
jobj1 <- job(q_obj=qobj, cmd = cmds, submission_type = "scatter", name = "job1")

## run the 10 commands sequentially, but WAIT for the previous job to complete
jobj2 <- job(q_obj=qobj, cmd = cmds, submission_type = "serial",
   dependency_type = "gather", previous_job = "job1")

fobj <- flow(jobs = list(jobj1, jobj2))

## plot the flow
plot_flow(fobj)
## **Not run**:
# ## dry run, only create the structure without submitting jobs
# submit_flow(fobj)
#
# ## execute the jobs: ONLY works on computing cluster, would fail otherwise
# submit_flow(fobj, execute = TRUE)
#
# ## **End(Not run)**

Aliases: job .. Keywords:

kill¶

Killing a pipline requires files which are created at the END of the submit_flow commands.

Description¶

Even if you want to kill the flow, its best to let submit_flow do its job, when done simply use kill(flow_wd). If submit_flow is interrupted, flow detail files etc are not created, thus flowr can’t associate submitted jobs with flow instance.

Usage¶

kill(x, ...)

## method for class 'character'
kill(x, force = FALSE, ...)

## method for class 'flow'
kill(x, kill_cmd, jobid_col = "job_sub_id", ...)

Arguments¶

x: either path to flow [character] or fobj object of class flow

...: not used
force: When killing multiple flows, force is neccesary. This makes sure multiple flows are killed by accident.
kill_cmd: The command used to kill. Default is ‘bkill’ (LSF). One can used qdel for ‘torque’, ‘sge’ etc.
jobid_col: Advanced use. The column name in ‘flow_details.txt’ file used to fetch jobids to kill

Examples¶

## **Not run**:
#
# ## example for terminal
# ## flowr kill_flow x=path_to_flow_directory
# ## In case path matches multiple folders, flowr asks before killing
# kill(x='fastq_haplotyper*')
#  Flowr: streamlining workflows
#  found multiple wds:
#  /fastq_haplotyper-MS132-20150825-16-24-04-0Lv1PbpI
#  /fastq_haplotyper-MS132-20150825-17-47-52-5vFIkrMD
#  Really kill all of them ? kill again with force=TRUE
#
# ## submitting again with force=TRUE will kill them:
# kill(x='fastq_haplotyper*', force = TRUE)
# ## **End(Not run)**

Aliases: kill kill.character kill.flow .. Keywords:

flowopts¶

Default options/params used in ngsflows and flowr

Description¶

There are three helper functions which attempt to manage params used by flowr and ngsflows: - get_opts OR opts_flow\$get(): show all default options - set_opts OR opts_flow\$set(): set default options - load_opts OR opts_flow\$load(): load options specified in a tab seperated text file

For more details regarding these funtions refer to params.

Usage¶

flowopts

opts_flow

Arguments¶

...

get: names of options to fetch

set: a set of options in a name=value format seperated by commas

Format¶

opts_flow Details ~~~~~~~~~~~~~~~~~~

By default flowr loads, ~/flowr/conf/flowr.conf and ~/flowr/conf/ngsflows.conf Below is a list of default flowr options, retrieved via opts_flow$get(): <pre>

|name |value | |:—————–|:————————| |default_regex |(.*) | |flow_base_path |~/flowr | |flow_conf_path |~/flowr/conf | |flow_parse_lsf |.*(<[0-9]*>).* | |flow_parse_moab |(.*) | |flow_parse_sge |(.*) | |flow_parse_slurm |(.*) | |flow_parse_torque |(.?)..* | |flow_pipe_paths |~/flowr/pipelines | |flow_pipe_urls |~/flowr/pipelines | |flow_platform |local | |flow_run_path |~/flowr/runs | |my_conf_path |~/flowr/conf | |my_dir |path/to/a/folder | |my_path |~/flowr | |my_tool_exe |/usr/bin/ls | |time_format |%a %b %e %H:%M:%S CDT %Y | |verbose |FALSE | </pre>

Examples¶

## Set options: set_opts()
opts = set_opts(flow_run_path = "~/mypath")
## OR if you would like to supply a long list of options:
opts = set_opts(.dots = list(flow_run_path = "~/mypath"))

## load options from a configuration file: load_opts()
myconfile = fetch_conf("flowr.conf")
load_opts(myconfile)
**Reading file, using 'V1' as id_column to remove empty rows.**<strong class='warning'>Warning message:


Seems like these paths do not exist, this may cause issues later:

</strong>

|name              |value                    |
|:-----------------|:------------------------|
|flow_parse_slurm  |(.*)                     |
|flow_parse_sge    |(.*)                     |
|flow_parse_lsf    |.*(\<[0-9]*\>).*         |
|flow_parse_torque |(.?)\..*                 |
|flow_pipe_urls    |~/flowr/pipelines        |
|flow_pipe_paths   |~/flowr/pipelines        |
|flow_conf_path    |~/flowr/conf             |
|flow_base_path    |~/flowr                  |
|var               |                         |
|time_format       |%a %b %e %H:%M:%S CDT %Y |

## Fetch options: get_opts()
get_opts("flow_run_path")
 flow_run_path
"~/flowr/runs"
get_opts()


|name              |value                    |
|:-----------------|:------------------------|
|flow_base_path    |~/flowr                  |
|flow_conf_path    |~/flowr/conf             |
|flow_parse_lsf    |.*(\<[0-9]*\>).*         |
|flow_parse_moab   |(.*)                     |
|flow_parse_sge    |(.*)                     |
|flow_parse_slurm  |(.*)                     |
|flow_parse_torque |(.?)\..*                 |
|flow_pipe_paths   |~/flowr/pipelines        |
|flow_pipe_urls    |~/flowr/pipelines        |
|flow_platform     |local                    |
|flow_run_path     |~/flowr/runs             |
|time_format       |%a %b %e %H:%M:%S CDT %Y |
|var               |                         |
|verbose           |FALSE                    |

Aliases: flowopts opts_flow .. Keywords:

datasets .. Author:

plot_flow¶

plot_flow

Description¶

plot the flow object

plot_flow.character: works on a flowdef file.

Usage¶

plot_flow(x, ...)

## method for class 'flow'
plot_flow(x, ...)

## method for class 'list'
plot_flow(x, ...)

## method for class 'character'
plot_flow(x, ...)

## method for class 'flowdef'
plot_flow(x, detailed = TRUE, type = c("1", "2"), pdf = FALSE, pdffile, ...)

Arguments¶

x: Object of class flow, or a list of flow objects or a flowdef

...: experimental
detailed: include some details
type: 1 is original, and 2 is a elipse with less details
pdf: create a pdf instead of plotting interactively
pdffile: output file name for the pdf file

Examples¶

qobj = queue(type="lsf")
cmds = rep("sleep 5", 10)
jobj1 <- job(q_obj=qobj, cmd = cmds, submission_type = "scatter", name = "job1")
jobj2 <- job(q_obj=qobj, name = "job2", cmd = cmds, submission_type = "scatter",
             dependency_type = "serial", previous_job = "job1")
fobj <- flow(jobs = list(jobj1, jobj2))
plot_flow(fobj)

### Gather: many to one relationship
jobj1 <- job(q_obj=qobj, cmd = cmds, submission_type = "scatter", name = "job1")
jobj2 <- job(q_obj=qobj, name = "job2", cmd = cmds, submission_type = "scatter",
             dependency_type = "gather", previous_job = "job1")
fobj <- flow(jobs = list(jobj1, jobj2))
plot_flow(fobj)

### Burst: one to many relationship
jobj1 <- job(q_obj=qobj, cmd = cmds, submission_type = "serial", name = "job1")
jobj2 <- job(q_obj=qobj, name = "job2", cmd = cmds, submission_type = "scatter",
             dependency_type = "burst", previous_job = "job1")
fobj <- flow(jobs = list(jobj1, jobj2))
plot_flow(fobj)

Aliases: plot_flow plot_flow.character plot_flow.flow plot_flow.flowdef plot_flow.list .. Keywords:

queue¶

Create a queue object which containg details about how a job is submitted.

Description¶

This function defines the queue used to submit jobs to the cluster. In essence details about the computing cluster in use.

Usage¶

queue(object, platform = c("local", "lsf", "torque", "sge", "moab"), format = "", queue = "long", walltime, memory, cpu = 1, extra_opts = "", submit_exe, nodes = "1", jobname = "name", email = Sys.getenv("USER"), dependency = list(), server = "localhost", verbose = FALSE, cwd = "", stderr = "", stdout = "", ...)

Arguments¶

object: this is not used currenlty, ignore.
platform: Required and important. Currently supported values are ‘lsf’ and ‘torque’. [Used by class job]
format: [advanced use] We have a default format for the final command line string generated for ‘lsf’ and ‘torque’.
queue: the type of queue your group usually uses

‘bsub’ etc.

walltime: max walltime of a job.
memory: The amount of memory reserved. Units depend on the platform used to process jobs
cpu: number of cpus you would like to reserve [Used by class job]
extra_opts: [advanced use] Extra options to be supplied while create the job submission string.
submit_exe: [advanced use] Already defined by ‘platform’. The exact command used to submit jobs to the cluster example ‘qsub’
nodes: [advanced use] number of nodes you would like to request. Or in case of torque name of the nodes.*optional* [Used by class job]
jobname: [debug use] name of this job in the computing cluster
email: [advanced use] Defaults to system user, you may put you own email though may get tons of them.
dependency: [debug use] a list of jobs to complete before starting this one
server: [not used] This is not implemented currently. This would specify the head node of the computing cluster. At this time submission needs to be done on the head node of the cluster where flow is to be submitted
verbose: [logical] TRUE/FALSE
cwd: [debug use] Ignore
stderr: [debug use] Ignore
stdout: [debug use] Ignore

...: other passed onto object creation. Example: memory, walltime, cpu

Details¶

Resources : Can be defined once using a queue object and recylced to all the jobs in a flow. If resources (like memory, cpu, walltime, queue) are supplied at the job level they overwrite the one supplied in queue Nodes: can be supplied ot extend a job across multiple nodes. This is purely experimental and not supported. Server : This a hook which may be implemented in future. Submission script The ‘platform’ variable defines the format, and submit_exe; however these two are avaible for someone to create a custom submission command.

Examples¶

qobj <- queue(platform='lsf')

Aliases: queue .. Keywords:

queue .. Author:

rerun¶

Re-run a pipeline in case of hardware or software failures.

Description¶

hardware no change required, simple rerun: rerun(x=flow_wd)
software either a change to flowmat or flowdef has been made: rerun(x=flow_wd, mat = new_flowmat, def = new_flowdef)

NOTE:

flow_wd: flow working directory, same input as used for status

Usage¶

rerun(x, ...)

## method for class 'character'
rerun(x, ...)

## method for class 'flow'
rerun(x, mat, def, start_from, execute = TRUE, kill = TRUE, ...)

Arguments¶

x: flow working directory

...: not used
mat: (optional) flowmat fetched from previous submission if missing. For more information regarding the format refer to to_flowmat
def: (optional) flowdef fetched from previous submission if missing. For more information regarding the format refer to to_flowdef
start_from: which job to start from, this is a job name.
execute: [logical] whether to execute or not
kill: (optional) logical indicating whether to kill the jobs from the previous execution of flow.

Details¶

This function fetches details regarding the previous execution from the flow working directory (flow_wd). It reads the flow object from the flow_details.rds file, and extracts flowdef and flowmat from it using to_flowmat and to_flowdef functions. New flowmat / flowdef for re-run: Optionally, if either of these (flowmat or flowdef) are supplied, supplied ones are used instead for the new submission. This functions efficiently updates job details of the latest submission into the previous file; thus information regarding previous job ids and their status is not lost.

Examples¶

## **Not run**:
# rerun_flow(wd = wd, fobj = fobj, execute = TRUE, kill = TRUE)
# ## **End(Not run)**

Aliases: rerun rerun.character rerun.flow .. Keywords:

run¶

run pipelines

Description¶

Running examples flows This wraps a few steps: Get all the commands to run (flow_mat) Create a flow object, using flow_mat and a default flowdef (picked from the same folder). Use submit_flow() to submit this to the cluster.

Usage¶

run(x, platform, def, flow_run_path = get_opts("flow_run_path"), execute = FALSE, ...)

run_pipe(x, platform, def, flow_run_path = get_opts("flow_run_path"), execute = FALSE, ...)

Arguments¶

x: name of the pipeline to run. This is a function called to create a flow_mat.
platform: what platform to use, overrides flowdef
def: flow definition
flow_run_path: passed onto to_flow. Default it picked up from flowr.conf. Typically this is ~/flowr/runs
execute: TRUE/FALSE

...: passed onto the pipeline function specified in x

Examples¶

Aliases: run run_flow run_pipe .. Keywords:

setup¶

Setup and initialize some scripts.

Description¶

Setup and initialize some scripts.

Usage¶

setup(bin = "~/bin", flow_base_path = get_opts("flow_base_path"))

Arguments¶

bin: path to bin folder
flow_base_path: the root folder for all flowr operations

Details¶

Will add more to this to identify cluster and aid in other things

Examples¶

Aliases: setup .. Keywords:

status¶

status

Description¶

Summarize status of executed flow(x)

Usage¶

status(x, out_format = "markdown")

get_status(x, ...)

## method for class 'character'
get_status(x, out_format = "markdown", ...)

## method for class 'data.frame'
get_status(x, ...)

## method for class 'flow'
get_status(x, out_format = "markdown", ...)

Arguments¶

x: path to the flow root folder or a parent folder to summarize several flows.
out_format: passed onto knitr:::kable. supports: markdown, rst, html...

...: not used

Details¶

basename(x) is used in a wild card search. - If x is a path with a single flow, it outputs the status of one flow. - If the path has more than one flow then this could give a summary of all of them. - Instead if x is supplied with paths to more than one flow, then this individually prints status of each. Alternatively, x can also be a flow object

Examples¶

## **Not run**:
# status(x = "~/flowr/runs/sleep_pipe*")
# ## an example for running from terminal
# flowr status x=path_to_flow_directory cores=6
# ## **End(Not run)**

Aliases: get_status get_status.character get_status.data.frame get_status.flow status .. Keywords:

submit_flow¶

submit_flow

Description¶

submit_flow

Usage¶

submit_flow(x, verbose = get_opts("verbose"), ...)

## method for class 'list'
submit_flow(x, verbose = get_opts("verbose"), ...)

## method for class 'flow'
submit_flow(x, verbose = get_opts("verbose"), execute = FALSE, uuid, plot = TRUE, dump = TRUE, .start_jid = 1, ...)

Arguments¶

x: a object of class flow.
verbose: logical.

...: Advanced use. Any additional parameters are passed on to submit_job function.
execute: logical whether or not to submit the jobs
uuid: character Advanced use. This is the final path used for flow execution.

Especially useful in case of re-running a flow.

plot: logical whether to make a pdf flow plot (saves it in the flow working directory).
dump: dump all the flow details to the flow path
.start_jid: Job to start this submission from. Advanced use, should be 1 by default.

Examples¶

## **Not run**:
# submit_flow(fobj = fobj, ... = ...)## **End(Not run)**

Aliases: submit_flow submit_flow.flow submit_flow.list .. Keywords:

test_queue¶

test_queue

Description¶

This function attempts to test the submission of a job to the queue. We would first submit one single job, then submit another with a dependency to see if configuration works. This would create a folder in home called ‘flows’.

Usage¶

test_queue(q_obj, verbose = TRUE, ...)

Arguments¶

q_obj: queue object
verbose: toggle

...: These params are passed onto queue. ?queue, for more information

Examples¶

## **Not run**:
# test_queue(q_obj = q_obj, ... = ...)## **End(Not run)**

Aliases: test_queue .. Keywords:

to_flow¶

Create flow objects

Description¶

Use a set of shell commands and flow definiton to create flow object.

vector: a file with flowmat table

a named list of commands for a sample. Its best to supply a flowmat instead.

Usage¶

to_flow(x, ...)

## method for class 'vector'
to_flow(x, def, grp_col, jobname_col, cmd_col, ...)

## method for class 'flowmat'
to_flow(x, def, grp_col, jobname_col, cmd_col, flowname, flow_run_path, platform, submit = FALSE, execute = FALSE, qobj, ...)

## method for class 'list'
to_flow(x, def, flowname, flow_run_path, desc, qobj, ...)

Arguments¶

x: path (char. vector) to flow_mat, a data.frame or a list.

...: Supplied to specific functions like to_flow.data.frame
def: A flow definition table. Basically a table with resource requirements and mapping of the jobs in this flow
grp_col: column name used to split x (flow_mat). Default: samplename
jobname_col: column name with job names. Default: jobname
cmd_col: column name with commands. Default: cmd
flowname: name of the flow
flow_run_path: Path to a folder. Main operating folder for this flow. Default it get_opts(“flow_run_path”).
platform: character vector, specifying the platform to use. local, lsf, torque, moab, sge, slurm, ...

This over-rides the platform column in flowdef.

submit: Depreciated. Use submit_flow on flow object this function returns. TRUE/FALSE
execute: Depreciated. Use submit_flow on flow object this function returns. TRUE/FALSE, an paramter to submit_flow()
qobj: Depreciated, modify <a href = ‘http://docs.flowr.space/en/latest/rd/vignettes/build-pipes.html#cluster-interface’>cluster templates</a> instead. A object of class queue.
desc: Advanced Use. final flow name, please don’t change.

Value¶

Returns a flow object. If execute=TRUE, fobj is rich with information about where and how the flow was executed. It would include details like jobids, path to exact scripts run etc. To use kill_flow, to kill all the jobs one would need a rich flow object, with job ids present. Behaviour: What goes in, and what to expect in return? - submit=FALSE & execute=FALSE: Create and return a flow object - submit=TRUE & execute=FALSE: dry-run, Create a flow object then, create a structured execution folder with all the commands - submit=TRUE, execute=TRUE: Do all of the above and then, submit to cluster

Details¶

The parameter x can be a path to a flow_mat, or a data.frame (as read by read_sheet). This is a minimum three column matrix with three columns: samplename, jobname and cmd

Examples¶

ex = file.path(system.file(package = "flowr"), "pipelines")
flowmat = as.flowmat(file.path(ex, "sleep_pipe.tsv"))
**mat seems to be a file, reading it...****Using `samplename` as the grouping column****Using `jobname` as the jobname column****Using `cmd` as the cmd column**flowdef = as.flowdef(file.path(ex, "sleep_pipe.def"))
**def seems to be a file, reading it...**fobj = to_flow(x = flowmat, def = flowdef, flowname = "sleep_pipe", platform = "lsf")
**Using flow_run_path default: ~/flowr/runs****
##--- Checking flow definition and flow matrix for consistency...****
##--- Detecting platform...****Will use platform from flow definition****Platform supplied, this will override defaults from flow definition...****
Working on... sample1****.****.****.****.**

Aliases: to_flow to_flow.flowmat to_flow.list to_flow.vector .. Keywords:

to_flowdef¶

Create a skeleton flow definition using a flowmat.

Description¶

This function enables creation of a skeleton flow definition with several default values, using a flowmat. To customize the flowdef, one may supply parameters such as sub_type and dep_type upfront. As such, these params must be of the same length as number of unique jobs using in the flowmat.

Usage¶

to_flowdef(x, ...)

## method for class 'flowmat'
to_flowdef(x, sub_type, dep_type, prev_jobs, queue = "short", platform = "torque", memory_reserved = "2000", cpu_reserved = "1", walltime = "1:00", ...)

## method for class 'flow'
to_flowdef(x, ...)

## method for class 'character'
to_flowdef(x, ...)

as.flowdef(x, ...)

is.flowdef(x)

Arguments¶

x: can a path to a flowmat, flomat or flow object.

...: not used
sub_type: submission type, one of: scatter, serial. Character, of length one or same as the number of jobnames
dep_type: dependency type, one of: gather, serial or burst. Character, of length one or same as the number of jobnames
prev_jobs: previous job name
queue: Cluster queue to be used
platform: platform of the cluster: lsf, sge, moab, torque, slurm etc.
memory_reserved: amount of memory required.
cpu_reserved: number of cpu’s required
walltime: amount of walltime required
x: can be a data.frame or a path for a flow definition file

...: passed onto check.flowdef

Examples¶

Aliases: as.flowdef is.flowdef to_flowdef to_flowdef.character to_flowdef.flow to_flowdef.flowmat .. Keywords:

to_flowdet¶

to_flowdet

Description¶

to_flowdet

get a flow_details file from the directory structure. This has less information than the one generated using a flow object. Lacks jobids etc...

Usage¶

to_flowdet(x, ...)

## method for class 'rootdir'
to_flowdet(x, ...)

## method for class 'character'
to_flowdet(x, ...)

## method for class 'flow'
to_flowdet(x, ...)

Arguments¶

x: this is a wd

...: not used

Details¶

if x is char. assumed a path, check if flow object exists in it and read it. If there is no flow object, try using a simpler function

Examples¶

Aliases: to_flowdet to_flowdet.character to_flowdet.flow to_flowdet.rootdir .. Keywords:

to_flowmat¶

Taking in a named list and returns a two columns data.frame

Description¶

Taking in a named list and returns a two columns data.frame

as.flowmat(): reads a file and checks for required columns. If x is data.frame checks for required columns.

Usage¶

to_flowmat(x, ...)

## method for class 'list'
to_flowmat(x, samplename, ...)

## method for class 'data.frame'
to_flowmat(x, ...)

## method for class 'flow'
to_flowmat(x, ...)

as.flowmat(x, grp_col, jobname_col, cmd_col, ...)

is.flowmat(x)

Arguments¶

x: a named list OR vector. Where name corresponds to the jobname and value is a vector of commands to run

...: not used
samplename: character of length 1 or that of nrow(x)
grp_col: column used for grouping, default samplename.
jobname_col: column specifying jobname, default jobname
cmd_col: column specifying commands to run, default cmd
x: a data.frame or path to file with flow details in it.

...: not used

Examples¶

Aliases: as.flowmat is.flowmat to_flowmat to_flowmat.data.frame to_flowmat.flow to_flowmat.list .. Keywords:

whisker_render¶

Wrapper around whisker.render with some sugar on it...

Description¶

This is a wrapper around whisker.render

Usage¶

whisker_render(template, data)

Arguments¶

template: template used
data: a list with variables to be used to fill in the template.

Examples¶

Aliases: whisker_render .. Keywords:

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