[med-svn] [snakemake] 01/05: Add snakemake manpage

Mon Sep 14 06:17:19 UTC 2015

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daube-guest pushed a commit to branch master
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commit bc4a2bb051271b91eac4a1e341f77627fcbee952
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Mon Sep 14 13:43:38 2015 +1000

    Add snakemake manpage
---
 debian/snakemake.1        | 343 ++++++++++++++++++++++++++++++++++++++++++++++
 debian/snakemake.manpages |   1 +
 2 files changed, 344 insertions(+)

diff --git a/debian/snakemake.1 b/debian/snakemake.1
new file mode 100644
index 0000000..818ce4b
--- /dev/null
+++ b/debian/snakemake.1
@@ -0,0 +1,343 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.2.
+.TH SNAKEMAKE "1" "September 2015" "snakemake 3.4.1" "User Commands"
+.SH NAME
+snakemake \- manual page for snakemake 3.4.1
+.SH DESCRIPTION
+usage: snakemake [\-h] [\-\-snakefile FILE] [\-\-gui [PORT]] [\-\-cores [N]]
+.IP
+[\-\-resources [NAME=INT [NAME=INT ...]]]
+[\-\-config [KEY=VALUE [KEY=VALUE ...]]] [\-\-configfile FILE]
+[\-\-list] [\-\-list\-target\-rules] [\-\-directory DIR] [\-\-dryrun]
+[\-\-printshellcmds] [\-\-dag] [\-\-rulegraph] [\-\-d3dag]
+[\-\-summary] [\-\-detailed\-summary] [\-\-touch] [\-\-keep\-going]
+[\-\-force] [\-\-forceall] [\-\-forcerun TARGET [TARGET ...]]
+[\-\-prioritize TARGET [TARGET ...]] [\-\-allow\-ambiguity]
+[\-\-cluster CMD | \fB\-\-cluster\-sync\fR CMD | \fB\-\-drmaa\fR [ARGS]]
+[\-\-cluster\-config FILE] [\-\-immediate\-submit]
+[\-\-jobscript SCRIPT] [\-\-jobname NAME] [\-\-reason]
+[\-\-stats FILE] [\-\-nocolor] [\-\-quiet] [\-\-nolock] [\-\-unlock]
+[\-\-cleanup\-metadata [FILE [FILE ...]]] [\-\-rerun\-incomplete]
+[\-\-ignore\-incomplete] [\-\-list\-version\-changes]
+[\-\-list\-code\-changes] [\-\-list\-input\-changes]
+[\-\-list\-params\-changes] [\-\-latency\-wait SECONDS]
+[\-\-wait\-for\-files [FILE [FILE ...]]] [\-\-benchmark\-repeats N]
+[\-\-notemp] [\-\-keep\-target\-files]
+[\-\-allowed\-rules ALLOWED_RULES [ALLOWED_RULES ...]]
+[\-\-timestamp] [\-\-greediness GREEDINESS] [\-\-print\-compilation]
+[\-\-overwrite\-shellcmd OVERWRITE_SHELLCMD] [\-\-verbose]
+[\-\-debug] [\-\-profile FILE] [\-\-bash\-completion] [\-\-version]
+[target [target ...]]
+.PP
+Snakemake is a Python based language and execution environment for GNU Makelike workflows.
+.SS "positional arguments:"
+.TP
+target
+Targets to build. May be rules or files.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-snakefile\fR FILE, \fB\-s\fR FILE
+The workflow definition in a snakefile.
+.TP
+\fB\-\-gui\fR [PORT]
+Serve an HTML based user interface to the given port
+(default: 8000). If possible, a browser window is
+opened.
+.TP
+\fB\-\-cores\fR [N], \fB\-\-jobs\fR [N], \fB\-j\fR [N]
+Use at most N cores in parallel (default: 1). If N is
+omitted, the limit is set to the number of available
+cores.
+.TP
+\fB\-\-resources\fR [NAME=INT [NAME=INT ...]], \fB\-\-res\fR [NAME=INT [NAME=INT ...]]
+Define additional resources that shall constrain the
+scheduling analogously to threads (see above). A
+resource is defined as a name and an integer value.
+E.g. \fB\-\-resources\fR gpu=1. Rules can use resources by
+defining the resource keyword, e.g. resources: gpu=1.
+If now two rules require 1 of the resource 'gpu' they
+won't be run in parallel by the scheduler.
+.TP
+\fB\-\-config\fR [KEY=VALUE [KEY=VALUE ...]]
+Set or overwrite values in the workflow config object.
+The workflow config object is accessible as variable
+config inside the workflow. Default values can be set
+by providing a JSON file (see Documentation).
+.TP
+\fB\-\-configfile\fR FILE
+Specify or overwrite the config file of the workflow
+(see the docs). Values specified in JSON or YAML
+format are available in the global config dictionary
+inside the workflow.
+.TP
+\fB\-\-list\fR, \fB\-l\fR
+Show availiable rules in given Snakefile.
+.TP
+\fB\-\-list\-target\-rules\fR, \fB\-\-lt\fR
+Show available target rules in given Snakefile.
+.TP
+\fB\-\-directory\fR DIR, \fB\-d\fR DIR
+Specify working directory (relative paths in the
+snakefile will use this as their origin).
+.TP
+\fB\-\-dryrun\fR, \fB\-n\fR
+Do not execute anything.
+.TP
+\fB\-\-printshellcmds\fR, \fB\-p\fR
+Print out the shell commands that will be executed.
+.TP
+\fB\-\-dag\fR
+Do not execute anything and print the directed acyclic
+graph of jobs in the dot language. Recommended use on
+Unix systems: snakemake \fB\-\-dag\fR | dot | display
+.TP
+\fB\-\-rulegraph\fR
+Do not execute anything and print the dependency graph
+of rules in the dot language. This will be less
+crowded than above DAG of jobs, but also show less
+information. Note that each rule is displayed once,
+hence the displayed graph will be cyclic if a rule
+appears in several steps of the workflow. Use this if
+above option leads to a DAG that is too large.
+Recommended use on Unix systems: snakemake \fB\-\-rulegraph\fR
+| dot | display
+.TP
+\fB\-\-d3dag\fR
+Print the DAG in D3.js compatible JSON format.
+.TP
+\fB\-\-summary\fR, \fB\-S\fR
+Print a summary of all files created by the workflow.
+The has the following columns: filename, modification
+time, rule version, status, plan. Thereby rule version
+contains the versionthe file was created with (see the
+version keyword of rules), and status denotes whether
+the file is missing, its input files are newer or if
+version or implementation of the rule changed since
+file creation. Finally the last column denotes whether
+the file will be updated or created during the next
+workflow execution.
+.TP
+\fB\-\-detailed\-summary\fR, \fB\-D\fR
+Print a summary of all files created by the workflow.
+The has the following columns: filename, modification
+time, rule version, input file(s), shell command,
+status, plan. Thereby rule version contains the
+versionthe file was created with (see the version
+keyword of rules), and status denotes whether the file
+is missing, its input files are newer or if version or
+implementation of the rule changed since file
+creation. The input file and shell command columns are
+selfexplanatory. Finally the last column denotes
+whether the file will be updated or created during the
+next workflow execution.
+.TP
+\fB\-\-touch\fR, \fB\-t\fR
+Touch output files (mark them up to date without
+really changing them) instead of running their
+commands. This is used to pretend that the rules were
+executed, in order to fool future invocations of
+snakemake. Fails if a file does not yet exist.
+.TP
+\fB\-\-keep\-going\fR, \fB\-k\fR
+Go on with independent jobs if a job fails.
+.TP
+\fB\-\-force\fR, \fB\-f\fR
+Force the execution of the selected target or the
+first rule regardless of already created output.
+.TP
+\fB\-\-forceall\fR, \fB\-F\fR
+Force the execution of the selected (or the first)
+rule and all rules it is dependent on regardless of
+already created output.
+.TP
+\fB\-\-forcerun\fR TARGET [TARGET ...], \fB\-R\fR TARGET [TARGET ...]
+Force the re\-execution or creation of the given rules
+or files. Use this option if you changed a rule and
+want to have all its output in your workflow updated.
+.TP
+\fB\-\-prioritize\fR TARGET [TARGET ...], \fB\-P\fR TARGET [TARGET ...]
+Tell the scheduler to assign creation of given targets
+(and all their dependencies) highest priority.
+(EXPERIMENTAL)
+.TP
+\fB\-\-allow\-ambiguity\fR, \fB\-a\fR
+Don't check for ambiguous rules and simply use the
+first if several can produce the same file. This
+allows the user to prioritize rules by their order in
+the snakefile.
+.TP
+\fB\-\-cluster\fR CMD, \fB\-c\fR CMD
+Execute snakemake rules with the given submit command,
+e.g. qsub. Snakemake compiles jobs into scripts that
+are submitted to the cluster with the given command,
+once all input files for a particular job are present.
+The submit command can be decorated to make it aware
+of certain job properties (input, output, params,
+wildcards, log, threads and dependencies (see the
+argument below)), e.g.: $ snakemake \fB\-\-cluster\fR 'qsub
+\fB\-pe\fR threaded {threads}'.
+.TP
+\fB\-\-cluster\-sync\fR CMD
+cluster submission command will block, returning the
+remote exitstatus upon remote termination (for
+example, this should be usedif the cluster command is
+\&'qsub \fB\-sync\fR y' (SGE)
+.TP
+\fB\-\-drmaa\fR [ARGS]
+Execute snakemake on a cluster accessed via DRMAA,
+Snakemake compiles jobs into scripts that are
+submitted to the cluster with the given command, once
+all input files for a particular job are present. ARGS
+can be used to specify options of the underlying
+cluster system, thereby using the job properties
+input, output, params, wildcards, log, threads and
+dependencies, e.g.: \fB\-\-drmaa\fR ' \fB\-pe\fR threaded {threads}'.
+Note that ARGS must be given in quotes and with a
+leading whitespace.
+.TP
+\fB\-\-cluster\-config\fR FILE, \fB\-u\fR FILE
+A JSON or YAML file that defines the wildcards used in
+\&'cluster'for specific rules, instead of having them
+specified in the Snakefile.For example, for rule 'job'
+you may define: { 'job' : { 'time' : '24:00:00' } } to
+specify the time for rule 'job'.
+.TP
+\fB\-\-immediate\-submit\fR, \fB\-\-is\fR
+Immediately submit all jobs to the cluster instead of
+waiting for present input files. This will fail,
+unless you make the cluster aware of job dependencies,
+e.g. via: $ snakemake \fB\-\-cluster\fR 'sbatch \fB\-\-dependency\fR
+{dependencies}. Assuming that your submit script (here
+sbatch) outputs the generated job id to the first
+stdout line, {dependencies} will be filled with space
+separated job ids this job depends on.
+.TP
+\fB\-\-jobscript\fR SCRIPT, \fB\-\-js\fR SCRIPT
+Provide a custom job script for submission to the
+cluster. The default script resides as 'jobscript.sh'
+in the installation directory.
+.TP
+\fB\-\-jobname\fR NAME, \fB\-\-jn\fR NAME
+Provide a custom name for the jobscript that is
+submitted to the cluster (see \fB\-\-cluster\fR). NAME is
+"snakejob.{rulename}.{jobid}.sh" per default. The
+wildcard {jobid} has to be present in the name.
+.TP
+\fB\-\-reason\fR, \fB\-r\fR
+Print the reason for each executed rule.
+.TP
+\fB\-\-stats\fR FILE
+Write stats about Snakefile execution in JSON format
+to the given file.
+.TP
+\fB\-\-nocolor\fR
+Do not use a colored output.
+.TP
+\fB\-\-quiet\fR, \fB\-q\fR
+Do not output any progress or rule information.
+.TP
+\fB\-\-nolock\fR
+Do not lock the working directory
+.TP
+\fB\-\-unlock\fR
+Remove a lock on the working directory.
+.TP
+\fB\-\-cleanup\-metadata\fR [FILE [FILE ...]], \fB\-\-cm\fR [FILE [FILE ...]]
+Cleanup the metadata of given files. That means that
+snakemake removes any tracked version info, and any
+marks that files are incomplete.
+.TP
+\fB\-\-rerun\-incomplete\fR, \fB\-\-ri\fR
+Re\-run all jobs the output of which is recognized as
+incomplete.
+.TP
+\fB\-\-ignore\-incomplete\fR, \fB\-\-ii\fR
+Ignore any incomplete jobs.
+.TP
+\fB\-\-list\-version\-changes\fR, \fB\-\-lv\fR
+List all output files that have been created with a
+different version (as determined by the version
+keyword).
+.TP
+\fB\-\-list\-code\-changes\fR, \fB\-\-lc\fR
+List all output files for which the rule body (run or
+shell) have changed in the Snakefile.
+.TP
+\fB\-\-list\-input\-changes\fR, \fB\-\-li\fR
+List all output files for which the defined input
+files have changed in the Snakefile (e.g. new input
+files were added in the rule definition or files were
+renamed). For listing input file modification in the
+filesystem, use \fB\-\-summary\fR.
+.TP
+\fB\-\-list\-params\-changes\fR, \fB\-\-lp\fR
+List all output files for which the defined params
+have changed in the Snakefile.
+.TP
+\fB\-\-latency\-wait\fR SECONDS, \fB\-\-output\-wait\fR SECONDS, \fB\-w\fR SECONDS
+Wait given seconds if an output file of a job is not
+present after the job finished. This helps if your
+filesystem suffers from latency (default 5).
+.TP
+\fB\-\-wait\-for\-files\fR [FILE [FILE ...]]
+Wait \fB\-\-latency\-wait\fR seconds for these files to be
+present before executing the workflow. This option is
+used internally to handle filesystem latency in
+cluster environments.
+.TP
+\fB\-\-benchmark\-repeats\fR N
+Repeat a job N times if marked for benchmarking
+(default 1).
+.TP
+\fB\-\-notemp\fR, \fB\-\-nt\fR
+Ignore temp() declarations. This is useful when
+running only a part of the workflow, since temp()
+would lead to deletion of probably needed files by
+other parts of the workflow.
+.TP
+\fB\-\-keep\-target\-files\fR
+Do not adjust the paths of given target files relative
+to the working directory.
+.TP
+\fB\-\-allowed\-rules\fR ALLOWED_RULES [ALLOWED_RULES ...]
+Only use given rules. If omitted, all rules in
+Snakefile are used.
+.TP
+\fB\-\-timestamp\fR, \fB\-T\fR
+Add a timestamp to all logging output
+.TP
+\fB\-\-greediness\fR GREEDINESS
+Set the greediness of scheduling. This value between 0
+and 1 determines how careful jobs are selected for
+execution. The default value (1.0) provides the best
+speed and still acceptable scheduling quality.
+.TP
+\fB\-\-print\-compilation\fR
+Print the python representation of the workflow.
+.TP
+\fB\-\-overwrite\-shellcmd\fR OVERWRITE_SHELLCMD
+Provide a shell command that shall be executed instead
+of those given in the workflow. This is for debugging
+purposes only.
+.TP
+\fB\-\-verbose\fR
+Print debugging output.
+.TP
+\fB\-\-debug\fR
+Allow to debug rules with e.g. PDB. This flag allows
+to set breakpoints in run blocks.
+.TP
+\fB\-\-profile\fR FILE
+Profile Snakemake and write the output to FILE. This
+requires yappi to be installed.
+.TP
+\fB\-\-bash\-completion\fR
+Output code to register bash completion for snakemake.
+Put the following in your .bashrc (including the
+accents): `snakemake \fB\-\-bash\-completion\fR` or issue it in
+an open terminal session.
+.TP
+\fB\-\-version\fR, \fB\-v\fR
+show program's version number and exit
diff --git a/debian/snakemake.manpages b/debian/snakemake.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/snakemake.manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snakemake.git

