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lib/BioX/Workflow/Plugin/Drake.pm view on Meta::CPAN
global:
- indir: /home/user/workflow
- outdir: /home/user/workflow/output
- file_rule: (.csv)$
rules:
- backup:
local:
- INPUT: "{$self->indir}/{$sample}.csv"
- OUTPUT: "{$self->outdir}/{$sample}.csv"
- thing: "other thing"
process: |
lib/BioX/Workflow/Plugin/Drake.pm view on Meta::CPAN
;
; Starting Workflow
;
;
; Starting backup
;
;
; Variables
; Indir: /home/guests/jir2004/workflow
; Outdir: /home/guests/jir2004/workflow/output/backup
; Local Variables:
; INPUT: {$self->indir}/{$sample}.csv
; OUTPUT: {$self->outdir}/{$sample}.csv
; thing: other thing
;
/home/guests/jir2004/workflow/output/backup/$[SAMPLE].csv <- /home/guests/jir2004/workflow/$[SAMPLE].csv
cp $INPUT $OUTPUT
;
; Ending backup
;
;
; Starting grep_VARA
lib/BioX/Workflow/Plugin/Drake.pm view on Meta::CPAN
Run drake
drake --workflow workflow.full.drake
The following steps will be run, in order:
1: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv [timestamped]
2: /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv [timestamped]
3: /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv [projected timestamped]
4: /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv [projected timestamped]
5: /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv [projected timestamped]
6: /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv [projected timestamped]
Confirm? [y/n] y
Running 6 steps with concurrence of 1...
--- 0. Running (timestamped): /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv
--- 0: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv -> done in 0.02s
--- 1. Running (timestamped): /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv
--- 1: /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv -> done in 0.01s
--- 2. Running (timestamped): /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv
Working on /home/user/workflow/output/backup/test1csv
--- 2: /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv -> done in 0.01s
--- 3. Running (timestamped): /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv
Working on /home/user/workflow/output/backup/test2csv
--- 3: /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv -> done in 0.01s
--- 4. Running (timestamped): /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv
--- 4: /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv -> done in 0.01s
--- 5. Running (timestamped): /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv
lib/BioX/Workflow/Plugin/Drake.pm view on Meta::CPAN
cat drake.log #Here is the log for the first run
2015-06-21 14:02:47,543 INFO Running 3 steps with concurrence of 1...
2015-06-21 14:02:47,568 INFO
2015-06-21 14:02:47,570 INFO --- 0. Running (timestamped): /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv
2015-06-21 14:02:47,592 INFO --- 0: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv -> done in 0.02s
#So on and so forth
If you look in the example directory you will see a few png files, these are outputs of the drake workflow.
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- outdir: data/processed
- file_rule: (.*)csv$
- plugins:
- FileExists
rules:
- backup:
local:
- wait: 0
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
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t/lib/TestsFor/BioX/Workflow/Test001.pm view on Meta::CPAN
global:
- indir: t/example/data/raw/test001
- outdir: t/example/data/processed/test001
- file_rule: (.*).csv\$
rules:
- backup:
process: cp {\$self->indir}/{\$sample}.csv {\$self->outdir}/{\$sample}.csv
- grep_VARA:
process: |
echo "Working on {\$self->{indir}}/{\$sample}.csv"
grep -i "VARA" {\$self->indir}/{\$sample}.csv >> {\$self->outdir}/{\$sample}.grep_VARA.csv
t/lib/TestsFor/BioX/Workflow/Test001.pm view on Meta::CPAN
my $cmd3 = <<EOF;
grep -i "VARB" {\$self->indir}/{\$sample}.grep_VARA.csv >> {\$self->outdir}/{\$sample}.grep_VARA.grep_VARB.csv
EOF
my $process_exp = [
{ backup => {
process =>
'cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv'
}
},
{ grep_VARA => { process => $cmd2 } },
t/lib/TestsFor/BioX/Workflow/Test001.pm view on Meta::CPAN
#return;
is( $got, $expected, "Got expected output!" );
ok( -d "$Bin/example/data/processed/test001" );
my @processes = qw(backup grep_VARA grep_VARB);
foreach my $process (@processes) {
ok( -d "$Bin/example/data/processed/test001/$process" );
}
}
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if(@file>0){
if($file[0]=~/\S\.[n]?fa/){ ## to handle .nfa and .fa files
$output_file = $file[0]; $out_file_name_provided=1;
if(-s $output_file){
rename($output_file, "$output_file\.bak");
print "\n# (INFO) $output_file is present. $output_file\.bak will be created for backup\n";
}
}elsif($file[0]=~/(\S+)\.\S+/){
$output_file = "$1\.fa"; $out_file_name_provided=1;
}
}else{ $output_file='default_out.fa'; }
my %correct_head_box_entry = %{&read_correct_head_box()};
for($p=0; $p < @file; $p++){
$in_file = $file[$p];
##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
## Make backup of the input file
##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
&cp( "$in_file", "$in_file\.bak$$");
print "\n $in_file\.bak$$ is created as a backup \n\n";
print chr(7);
##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
## Open files
##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
view release on metacpan or search on metacpan
MANIFEST.SKIP view on Meta::CPAN
# Avoid Module::Build generated and utility files.
\bBuild$
\b_build
# Avoid temp and backup files.
~$
\.gz$
\.old$
\.bak$
\.swp$
view release on metacpan or search on metacpan
lib/Bitcoin/Crypto/Key/ExtPrivate.pm view on Meta::CPAN
=head1 DESCRIPTION
This class allows you to create an extended private key instance. Extended keys
can be used to securely generate as many addresses as needed through key
derivation. This allows for long-term, reusable wallet with a single backup.
Moreover, you can use an extended private key to:
=over
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av_top_index|5.017009|5.003007|p
av_top_index_skip_len_mg|5.025010||Viu
av_undef|5.003007|5.003007|
av_unshift|5.003007|5.003007|
ax|5.003007|5.003007|
backup_one_GCB|5.025003||Viu
backup_one_LB|5.023007||Viu
backup_one_SB|5.021009||Viu
backup_one_WB|5.021009||Viu
bad_type_gv|5.019002||Viu
bad_type_pv|5.016000||Viu
BADVERSION|5.011004||Viu
BASEOP|5.003007||Viu
BhkDISABLE|5.013003||xV
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[Improvements]
- Major refactoring
0.009
- fix minor documentation bugs
- tuple signature check
- remove tidy backup and cache
0.008
- private methods, correct package name
0.007
- remove required test dependencies
0.006
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src/boost/utility/value_init.hpp
src/boost/variant/apply_visitor.hpp
src/boost/variant/detail/apply_visitor_binary.hpp
src/boost/variant/detail/apply_visitor_delayed.hpp
src/boost/variant/detail/apply_visitor_unary.hpp
src/boost/variant/detail/backup_holder.hpp
src/boost/variant/detail/bool_trait_def.hpp
src/boost/variant/detail/bool_trait_undef.hpp
src/boost/variant/detail/cast_storage.hpp
src/boost/variant/detail/config.hpp
src/boost/variant/detail/enable_recursive_fwd.hpp
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include/boost/variant/apply_visitor.hpp
include/boost/variant/bad_visit.hpp
include/boost/variant/detail/apply_visitor_binary.hpp
include/boost/variant/detail/apply_visitor_delayed.hpp
include/boost/variant/detail/apply_visitor_unary.hpp
include/boost/variant/detail/backup_holder.hpp
include/boost/variant/detail/bool_trait_def.hpp
include/boost/variant/detail/bool_trait_undef.hpp
include/boost/variant/detail/cast_storage.hpp
include/boost/variant/detail/config.hpp
include/boost/variant/detail/enable_recursive.hpp
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lib/Bot/BasicBot/Pluggable/Module/Excuse.pm view on Meta::CPAN
SIMM crosstalk.
IRQ dropout
Collapsed Backbone
Power company testing new voltage spike (creation) equipment
operators on strike due to broken coffee machine
backup tape overwritten with copy of system manager's favourite CD
UPS interrupted the server's power
The electrician didn't know what the yellow cable was so he yanked the ethernet out.
The keyboard isn't plugged in
The air conditioning water supply pipe ruptured over the machine room
The electricity substation in the car park blew up.
lib/Bot/BasicBot/Pluggable/Module/Excuse.pm view on Meta::CPAN
Change your language to Finnish.
Fluorescent lights are generating negative ions. If turning them off doesn't work, take them out and put tin foil on the ends.
High nuclear activity in your area.
What office are you in? Oh, that one. Did you know that your building was built over the universities first nuclear research site? And wow, aren't you the lucky one, your office is right over where the core is buried!
The MGs ran out of gas.
The UPS doesn't have a battery backup.
Recursivity. Call back if it happens again.
Someone thought The Big Red Button was a light switch.
The mainframe needs to rest. It's getting old, you know.
I'm not sure. Try calling the Internet's head office -- it's in the book.
The lines are all busy (busied out, that is -- why let them in to begin with?).
lib/Bot/BasicBot/Pluggable/Module/Excuse.pm view on Meta::CPAN
Root name servers corrupted.
Budget cuts forced us to sell all the power cords for the servers.
Someone hooked the twisted pair wires into the answering machine.
Operators killed by year 2000 bug bite.
We've picked COBOL as the language of choice.
Operators killed when huge stack of backup tapes fell over.
Robotic tape changer mistook operator's tie for a backup tape.
Someone was smoking in the computer room and set off the halon systems.
Your processor has taken a ride to Heaven's Gate on the UFO behind Hale-Bopp's comet.
it's an ID-10-T error
Dyslexics retyping hosts file on servers
The Internet is being scanned for viruses.
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lib/Bot/BasicBot/Pluggable/Module/Notify.pm view on Meta::CPAN
Each line in the file should consist of 3 fields. The first being the 'nick',
the second being the ident of the account connection, and the third being the
email address to send mail to.
The connection ident is optional, and only used as a backup check in the event
that the user may be roaming and their nick may be automatically switched to
something like '_barbie' instead of 'barbie'. An connection ident is used
within a regex pattern, but should not be a regex itself. Any regex characters
will be treated as literal string characters.
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bin/bot-basicbot-pluggable-infobot-upgrade view on Meta::CPAN
unless (-e "Infobot.storable") {
die "I can't see Infobot.storable in ./\n";
}
if (-e "Infobot.storable.backup") {
die "There's already a backup of Infobot.storable in ./\n";
}
cp("Infobot.storable", "Infobot.storable.backup")
or die "Can't back up Infobot.storable: $!\n";
unless (-s "Infobot.storable" == -s "Infobot.storable.backup") {
die "Infobot.storable backup isn't the same size!\n"
}
my $data = retrieve("Infobot.storable")
or die "Can't load Infobot.storable for some reason\n";
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MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
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examples/classes/Admin/apt/init.yml
examples/classes/Admin/apt/popcon.yml
examples/classes/Admin/apt/tools/changes.yml
examples/classes/Admin/apt/tools/init.yml
examples/classes/Admin/auto.yml
examples/classes/Admin/backup/init.yml
examples/classes/Admin/backup/remote.yml
examples/classes/Admin/base.yml
examples/classes/Admin/disk/lvm.yml
examples/classes/Admin/etc/functions.yml
examples/classes/Admin/etc/track.yml
examples/classes/Admin/harden/account/init.yml
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lib/Brackup/Target/Gmail.pm view on Meta::CPAN
# returns bool
sub has_chunk {
my ($self, $chunk) = @_;
my $dig = $chunk->backup_digest; # "sha1:sdfsdf" format scalar
if (my $dbh = $self->{dbh}) {
my $ans = $dbh->selectrow_array("SELECT COUNT(*) FROM ${CACHE_TABLE} WHERE key=?", undef, $dig);
warn "gmail database for $dig is = $ans\n";
return 1 if $ans;
lib/Brackup/Target/Gmail.pm view on Meta::CPAN
sub store_chunk {
my ($self, $chunk) = @_;
my ($fh, $filename) = tempfile( UNLINK => 1 );
print $fh ${ $chunk->chunkref };
close($fh);
$self->{_gmail}->store($filename, $chunk->backup_digest);
}
sub store_backup_meta {
my ($self, $name, $file) = @_;
my ($fh, $filename) = tempfile( UNLINK => 1 );
print $fh $file;
close($fh);
$self->{_gmail}->store($filename, $name);
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lib/Brackup.pm view on Meta::CPAN
__END__
=head1 NAME
Brackup - Flexible backup tool. Slices, dices, encrypts, and sprays across the net.
=head1 FURTHER READING
L<Brackup::Manual::Overview>
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t/05-defaults.t view on Meta::CPAN
# Test that defaults don't apply to required parameters that fail
$b->register_schema('required_no_default', {
params => {
name => { required => 1 },
backup_name => { default => 'unnamed' }
}
});
{
my $params = {}; # Missing required name
my $rejects = $b->process('required_no_default', $params);
is($rejects, { name => { required => 1 } }, 'Required parameter failure');
is($params->{backup_name}, 'unnamed', 'Default still applied to non-required params');
}
# Edge case: empty string and zero values should not trigger defaults
$b->register_schema('edge_cases', {
params => {
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the source repository: L<https://github.com/briandfoy/brick>
If you find a problem, file a ticket in the L<issue
tracker|https://github.com/briandfoy/brick/issues>.
There are also backup repositories hosted on other services. These
reflect the state of the main repo and exist only for redundancy:
=over 4
=item * L<https://bitbucket.com/briandfoy/brick>
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MANIFEST.SKIP view on Meta::CPAN
\bbuild.com$
# and Module::Build::Tiny generated files
\b_build_params$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
view release on metacpan or search on metacpan
MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
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MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
view release on metacpan or search on metacpan
MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
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lib/Bundler/MultiGem/Model/Gem.pm view on Meta::CPAN
}
=head2 process_single_file
Manipulates each file as follows:
* create a backup of the original file C<.bak>
* replace gem name reference with gem vname (C<foo> with C<v010-foo>)
* replace gem main_module reference with gem vmodule_name (C<Foo> with C<V010::Foo>)
* unlink the backup C<.bak>
=cut
sub process_single_file {
my ($self, $v, $f) = @_;
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MANIFEST.SKIP view on Meta::CPAN
CPAN.SKIP
t/000_standard__*
Debian_CPANTS.txt
nytprof.out
# Temp, old, emacs, vim, backup files.
~$
\.old$
\.swp$
\.tar$
\.tar\.gz$
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MANIFEST.SKIP view on Meta::CPAN
# Avoid Module::Build generated and utility files.
\bBuild$
\b_build/
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
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MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
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MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
view release on metacpan or search on metacpan
MANIFEST.SKIP view on Meta::CPAN
\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$
view release on metacpan or search on metacpan
MANIFEST.SKIP view on Meta::CPAN
\bbuild.com$
# and Module::Build::Tiny generated files
\b_build_params$
# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$