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commit bc4a2bb051271b91eac4a1e341f77627fcbee952 Author: Kevin Murray <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
