File Coverage

blib/lib/HPC/Runner/Command.pm
Criterion Covered Total %
statement 6 6 100.0
branch n/a
condition n/a
subroutine 2 2 100.0
pod n/a
total 8 8 100.0


line stmt bran cond sub pod time code
1             package HPC::Runner::Command;
2              
3 2     2   972655 use MooseX::App qw(Color);
  2         1829432  
  2         10  
4              
5             with 'BioSAILs::Utils::Plugin';
6             with 'BioSAILs::Utils::LoadConfigs';
7              
8 2     2   2682960 use MooseX::Types::Path::Tiny qw/Path Paths AbsPath AbsFile/;
  2         985233  
  2         31  
9              
10             option '+config_base' => ( default => '.hpcrunner', );
11              
12             =head3 project
13              
14             When submitting jobs we will prepend the jobname with the project name
15              
16             =cut
17              
18             option 'project' => (
19             is => 'rw',
20             isa => 'Str',
21             documentation => 'Give your jobnames an additional project name. '
22             . '#HPC jobname=gzip will be submitted as 001_project_gzip',
23             required => 0,
24             predicate => 'has_project',
25             cmd_aliases => ['p'],
26             );
27              
28             option 'no_log_json' => (
29             traits => ['Bool'],
30             is => 'rw',
31             isa => 'Bool',
32             default => 0,
33             documentation => 'Opt out of writing the tar archive of JSON stats. '
34             . 'This may be desirable for especially large workflows.',
35             );
36              
37             has 'submission_uuid' => (
38             is => 'rw',
39             isa => 'Str',
40             required => 0,
41             predicate => 'has_submissions_uuid',
42             );
43              
44             our $VERSION = '3.2.10';
45              
46             app_strict 0;
47              
48             sub BUILD { }
49              
50             =encoding utf-8
51              
52             =head1 NAME
53              
54             =begin HTML
55              
56             <p><img
57             src="http://github.com/jerowe/HPC-Runner-Command/blob/master/_docs/images/rabbit.jpeg"
58             width="500" height="250" alt="HPC::Runner::Command" /></p>
59              
60             =end HTML
61              
62             HPC::Runner::Command - Create composable bioinformatics hpc analyses.
63              
64             =head1 SYNOPSIS
65              
66             To create a new project
67              
68             hpcrunner.pl new MyNewProject
69              
70             To submit jobs to a cluster
71              
72             hpcrunner.pl submit_jobs --infile my_submission.sh
73              
74             To run jobs on an interactive queue or workstation
75              
76             hpcrunner.pl single_node --infile my_submission.sh
77              
78             =head1 DESCRIPTION
79              
80             HPC::Runner::Command is a set of libraries for scaffolding data analysis projects,
81             submitting and executing jobs on an HPC cluster or workstation, and obsessively
82             logging results.
83              
84             Get help by heading on over to github and raising an issue. L<GitHub |
85             https://github.com/biosails/HPC-Runner-Command/issues>.
86              
87             Please see the complete documentation at L<HPC::Runner::Command GitBooks |
88             https://jerowe.gitbooks.io/hpc-runner-command-docs/content/>.
89              
90             =head1 Quick Start - Create a New Project
91              
92             You can create a new project, with a sane directory structure by using
93              
94             hpcrunner.pl new MyNewProject
95              
96             =head1 Quick Start - Submit Workflows
97              
98             =head2 Simple Example
99              
100             Our simplest example is a single job type with no dependencies - each task is
101             independent of all other tasks.
102              
103             =head3 Workflow file
104              
105             #preprocess.sh
106              
107             echo "preprocess" && sleep 10;
108             echo "preprocess" && sleep 10;
109             echo "preprocess" && sleep 10;
110              
111             =head3 Submit to the scheduler
112              
113             hpcrunner.pl submit_jobs --infile preprocess.sh
114              
115             =head3 Look at results!
116              
117             tree hpc-runner
118              
119             =head3 Audit your results
120              
121             hpcrunner.pl stats -h
122             hpcrunner.pl stats
123              
124             =head2 Job Type Dependencency Declaration
125              
126             Most of the time we have jobs that depend upon other jobs.
127              
128             =head3 Workflow file
129              
130             #blastx.sh
131              
132             #HPC jobname=unzip
133             unzip Sample1.zip
134             unzip Sample2.zip
135             unzip Sample3.zip
136              
137             #HPC jobname=blastx
138             #HPC deps=unzip
139             blastx --db env_nr --sample Sample1.fasta
140             blastx --db env_nr --sample Sample2.fasta
141             blastx --db env_nr --sample Sample3.fasta
142              
143             =head3 Submit to the scheduler
144              
145             hpcrunner.pl submit_jobs --infile preprocess.sh
146              
147             =head3 Look at results!
148              
149             tree hpc-runner
150              
151             =head2 Task Dependencency Declaration
152              
153             Within a job type we can declare dependencies on particular tasks.
154              
155             =head3 Workflow file
156              
157             #blastx.sh
158              
159             #HPC jobname=unzip
160             #TASK tags=Sample1
161             unzip Sample1.zip
162             #TASK tags=Sample2
163             unzip Sample2.zip
164             #TASK tags=Sample3
165             unzip Sample3.zip
166              
167             #HPC jobname=blastx
168             #HPC deps=unzip
169             #TASK tags=Sample1
170             blastx --db env_nr --sample Sample1.fasta
171             #TASK tags=Sample2
172             blastx --db env_nr --sample Sample2.fasta
173             #TASK tags=Sample3
174             blastx --db env_nr --sample Sample3.fasta
175              
176             =head3 Submit to the scheduler
177              
178             hpcrunner.pl submit_jobs --infile preprocess.sh
179              
180             =head3 Look at results!
181              
182             tree hpc-runner
183              
184             =head3 Audit your results
185              
186             hpcrunner.pl stats -h
187             hpcrunner.pl stats
188              
189             =cut
190              
191             =head2 Declare Scheduler Variables
192              
193             Each scheduler has its own set of variables. HPC::Runner::Command has a set of
194             generalized variables for declaring types across templates. For more information
195             please see L<Job Scheduler
196             Comparison|https://jerowe.gitbooks.io/hpc-runner-command-docs/content/job_submission/comparison.html>
197              
198             Additionally, for workflows with a large number of tasks, please see
199             L<Considerations for Workflows with a Large Number of
200             Tasks|https://jerowe.gitbooks.io/hpc-runner-command-docs/content/design_workflow.html#considerations-for-workflows-with-a-large-number-of-tasks>
201             for information on how to group tasks together.
202              
203             =head3 Workflow file
204              
205             #blastx.sh
206              
207             #HPC jobname=unzip
208             #HPC cpus_per_task=1
209             #HPC partition=serial
210             #HPC commands_per_node=1
211             #HPC mem=4GB
212             #TASK tags=Sample1
213             unzip Sample1.zip
214             #TASK tags=Sample2
215             unzip Sample2.zip
216             #TASK tags=Sample3
217             unzip Sample3.zip
218              
219             #HPC jobname=blastx
220             #HPC cpus_per_task=6
221             #HPC deps=unzip
222             #TASK tags=Sample1
223             blastx --threads 6 --db env_nr --sample Sample1.fasta
224             #TASK tags=Sample2
225             blastx --threads 6 --db env_nr --sample Sample2.fasta
226             #TASK tags=Sample3
227             blastx --threads 6 --db env_nr --sample Sample3.fasta
228              
229             =head3 Submit to the scheduler
230              
231             hpcrunner.pl submit_jobs --infile preprocess.sh
232              
233             =head3 Look at results!
234              
235             tree hpc-runner
236              
237             =head3 Audit your results
238              
239             hpcrunner.pl stats -h
240             hpcrunner.pl stats
241              
242             =cut
243              
244             __PACKAGE__->meta()->make_immutable();
245              
246             1;
247              
248             __END__
249              
250             =head1 AUTHOR
251              
252             Jillian Rowe E<lt>jillian.e.rowe@gmail.comE<gt>
253              
254             =head1 Previous Release
255              
256             This software was previously released under L<HPC::Runner>.
257             L<HPC::Runner::Command> is a complete rewrite of the existing library. While it
258             is meant to have much of the same functionality, it is not backwords compatible.
259              
260             =head1 Acknowledgements
261              
262             As of Version 2.41:
263              
264             This modules continuing development is supported by NYU Abu Dhabi in the Center
265             for Genomics and Systems Biology. With approval from NYUAD, this information was
266             generalized and put on github, for which the authors would like to express
267             their gratitude.
268              
269             Before Version 2.41
270              
271             This module was originally developed at and for Weill Cornell Medical College in
272             Qatar within ITS Advanced Computing Team. With approval from WCMC-Q, this
273             information was generalized and put on github, for which the authors would like
274             to express their gratitude.
275              
276             =head1 COPYRIGHT
277              
278             Copyright 2016- Jillian Rowe
279              
280             =head1 LICENSE
281              
282             This library is free software; you can redistribute it and/or modify
283             it under the same terms as Perl itself.
284              
285             =head1 SEE ALSO
286              
287             =cut