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use Bio::SeqIO;
use File::Spec::Functions;
use File::Temp qw/ tempdir tempfile /;
use Fatal qw/ open mkdir chmod /;
use Test::More;
use Test::Exception;
use IPC::Cmd qw/ can_run /;
my $permdir = catdir( $tempdir, 'permdir' );
mkdir $permdir;
my $fs3 = Bio::BLAST::Database->open( full_file_basename => catfile( $permdir, 'foo'), type => 'nucleotide', write => 1);
ok(! $fs3->check_format_permissions, 'check_format_permissions OK for ffbn in new dir' );
ok( ! $fs3->is_split, 'returns false for is_split');
chmod 0444,$permdir;
my $perr = $fs3->check_format_permissions;
ok($perr, 'check_format_permissions returns bad for ffbn in non-writable' );
like( $perr, qr/directory/i, 'permissions error mentions directory');
throws_ok {
Bio::BLAST::Database->open( full_file_basename => catfile( $permdir, 'foo' ),
type => 'nucleotide',
write => 1,
);
} qr/writable/, 'new() should die if ffbn is not writable';
chmod 0744,$permdir;
ok(! $fs3->check_format_permissions, 'check_format_permissions OK again' );
my $test_seq_file = catfile( $DATADIR, "blastdb_test.nucleotide.seq" );
$fs3->format_from_file( seqfile => $test_seq_file );
my @newfiles = $fs3->list_files;
is( scalar @newfiles, 3, 'format succeeded in new dir' );
ok(! $fs3->check_format_permissions, 'check_format_permissions still OK after new format' );
foreach my $f (@newfiles) {
chmod 0444,$f;
my $perr2 = $fs3->check_format_permissions;
like( $perr2, qr/$f/, 'perm error mentions file');
}
chmod 0744, $_ for @newfiles;
ok(! $fs3->check_format_permissions, 'and then it comes back OK after all are writable again' );
# now test formatting it yet again
$fs3->format_from_file( seqfile => $test_seq_file );
is( scalar @newfiles, 3, 'format succeeded again' );
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install_util/BioStudioInstall.pm view on Meta::CPAN
{
my $self = shift;
$self->SUPER::ACTION_install;
my $confpath = $self->config_data('conf_path');
$confpath = $self->_endslash($confpath);
my $command = "chmod -R 777 $confpath*";
print $command, "\n";
system $command;
print "\n";
}
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t/GenBank.t view on Meta::CPAN
# Real batch retrieval using epost/efetch
# these tests may change if integrated further into Bio::DB::Gen*
# Currently only useful for retrieving GI's via get_seq_stream
$gb = Bio::DB::GenBank->new(%params);
eval {$seqin = $gb->get_seq_stream(-uids => [4887706 ,431229, 147460], -mode => 'batch');};
skip "Couldn't connect to complete GenBank batchmode epost/efetch tests. Skipping those tests: $@", 8 if $@;
my %result = ('M59757' => 12611 ,'X76083'=> 3140, 'J01670'=> 1593);
my $ct = 0;
# Test number is labile (dependent on remote results)
while ($seq = $seqin->next_seq) {
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GMOD/Admin/Update.pm view on Meta::CPAN
unless (-e "$full_path") {
$self->logit(-msg => "Creating temporary directory at $full_path");
my $command = <<END;
mkdir -p $full_path
chmod -R 0775 $full_path
END
;
my $result = system($command);
if ($result == 0) {
$self->logit(-msg => "Successfully created temporary directory");
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Makefile.PL view on Meta::CPAN
}
}
}
close(OUT);
close(IN);
chmod(0775,$outfile);
`$outfile`;
die "Couldn't run $outfile: $!"
if $?;
}
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lib/Bio/Graphics/Panel.pm view on Meta::CPAN
server user. For example, if your web server's document root is
located at /var/www/html, you might want to create a directory named
"tmpimages" for this purpose:
mkdir /var/www/html/tmpimages
chmod 1777 /var/www/html/tmpimages
The 1777 privilege will allow anyone to create files and
subdirectories in this directory, but only the owner of the file will
be able to delete it.
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lib/Bio/Grid/Run/SGE/Log/Analysis.pm view on Meta::CPAN
open my $cmd_fh, '>', $cmd_f or confess "Can't open filehandle: $!";
print $cmd_fh $self->restart_script;
$cmd_fh->close;
chmod 0755, $cmd_f;
my $log_f = $self->failed_log_file;
open my $log_fh, '>', $log_f or confess "Can't open filehandle: $!";
lib/Bio/Grid/Run/SGE/Log/Analysis.pm view on Meta::CPAN
open my $update_log_fh, '>', $update_log_file or confess "Can't open filehandle: $!";
print $update_log_fh join( " ", "cd", "'" . $conf->{working_dir} . "'", '&&', @post_log_cmd ), "\n";
$update_log_fh->close;
chmod 0755, $update_log_file;
return;
}
__PACKAGE__->meta->make_immutable();
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scripts/Data/psi-mi.obo view on Meta::CPAN
id: MI:0849
name: ncbi taxonomy
def: "The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and s...
subset: PSI-MI slim
xref: id-validation-regexp:\"[0-9\]+\"
xref: search-url: "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock"
is_a: MI:0473 ! participant database
[Term]
id: MI:0850
name: encode
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doc/Tutorial.pod view on Meta::CPAN
Make an executable script (note where the semi-colon and >> symbol are used)
system$ echo '#!/usr/bin/env perl' > my_script.pl
system$ echo 'print "hello!\n"; ' >> my_script.pl
system$ echo 'exit;' >> my_script.pl
system$ chmod +x my_script.pl
system$ cat my_script.pl
#!/usr/bin/env perl
print "hello!\n";
exit;
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script/phylotastic.PL view on Meta::CPAN
# run the tool
$class->run;
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
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lib/Bio/Tools/Run/Alignment/Clustalw.pm view on Meta::CPAN
$param_string .= " $infile2";
}
if ($command =~ /profile/) {
$instring = "-profile1=$infile1 -profile2=$infile2";
chmod 0777, $infile1, $infile2;
$command = '-profile';
}
if ($command =~ /add_sequences/) {
$instring = "-profile1=$infile1 -profile2=$infile2";
chmod 0777, $infile1,$infile2;
$command = '-sequences';
}
if ($command =~ /tree/) {
if( $^O eq 'dec_osf' ) {
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lib/Bio/VertRes/Config/CommandLine/LogParameters.pm view on Meta::CPAN
open( my $fh, '+>>', $self->log_file )
or Bio::VertRes::Config::Exceptions::FileCantBeModified->throw(
error => 'Couldnt open file for writing ' . $self->log_file );
print {$fh} $self->_output_string;
close($fh);
chmod $mode, $self->log_file;
return 1;
}
__PACKAGE__->meta->make_immutable;
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# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = YES
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
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Makefile.old view on Meta::CPAN
# --- MakeMaker tool_xsubpp section:
# --- MakeMaker tools_other section:
SHELL = /bin/sh
CHMOD = chmod
CP = cp
MV = mv
NOOP = $(TRUE)
NOECHO = @
RM_F = rm -f
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Bio/Root/IO.pm view on Meta::CPAN
if ( -d _ ) {
# notabene: 0777 is for making readable in the first place,
# it's also intended to change it to writable in case we have
# to recurse in which case we are better than rm -rf for
# subtrees with strange permissions
chmod(0777, ($Is_VMS ? VMS::Filespec::fileify($root) : $root))
or $self->warn("Could not make directory '$root' read+writable: $!")
unless $safe;
if (opendir DIR, $root){
@files = readdir DIR;
closedir DIR;
Bio/Root/IO.pm view on Meta::CPAN
if ($safe &&
($Is_VMS ? !&VMS::Filespec::candelete($root) : !-w $root)) {
print "skipped '$root'\n" if $verbose;
next;
}
chmod 0777, $root
or $self->warn("Could not make directory '$root' writable: $!")
if $force_writable;
print "rmdir '$root'\n" if $verbose;
if (rmdir $root) {
++$count;
}
else {
$self->warn("Could not remove directory '$root': $!");
chmod($rp, ($Is_VMS ? VMS::Filespec::fileify($root) : $root))
or $self->warn("and can't restore permissions to "
. sprintf("0%o",$rp) . "\n");
}
}
else {
Bio/Root/IO.pm view on Meta::CPAN
: !(-l $root || -w $root))
) {
print "skipped '$root'\n" if $verbose;
next;
}
chmod 0666, $root
or $self->warn( "Could not make file '$root' writable: $!")
if $force_writable;
warn "unlink '$root'\n" if $verbose;
# delete all versions under VMS
for (;;) {
unless (unlink $root) {
$self->warn("Could not unlink file '$root': $!");
if ($force_writable) {
chmod $rp, $root
or $self->warn("and can't restore permissions to "
. sprintf("0%o",$rp) . "\n");
}
last;
}
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lib/BioX/Workflow/Plugin/Drake.pm view on Meta::CPAN
EOF
}
close $fh;
chmod 0777, 'run-workflow.sh';
$self->samples(["\$SAMPLE"]);
};
=head3 write_process
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lib/BioX/Workflow/StructureOutput.pm view on Meta::CPAN
EOF
}
close $fh;
chmod 0777, 'run-workflow.sh';
$self->samples( ["\${SAMPLE}"] );
}
=head3 process_by_sample_outdir
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# --- MakeMaker tool_xsubpp section:
# --- MakeMaker tools_other section:
SHELL = /bin/sh
CHMOD = chmod
CP = cp
MV = mv
NOOP = $(TRUE)
NOECHO = @
RM_F = rm -f
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# Category :
# Version : 1.0
#------------------------------------------------------------------------------
sub get_perl_keywords{
my(%perl_keywords);
my @keywords=qw( AUTOLOAD BEGIN CORE DESTROY END abs accept alarm and atan2 bind binmode bless caller chdir chmod chop chown chr chroot
close closedir cmp connect continue cos crypt dbmclose dbmopen defined delete die do dump each else elsif endgrent endhostent endnetent endprotoent endpwent endservent
eof eq eval exec exit exp fcntl fileno flock for foreach fork format formline ge getc getgrent getgrgid getgrnam gethostbyaddr gethostbyname gethostent getlogin
getnetbyaddr getnetbyname getnetent getpeername getpgrp getppid getpriority getprotobyname getprotobynumber getprotoent getpwent getpwnam getpwuid getservbyname
getservbyport getservent getsockname getsockopt glob gmtime goto grep gt hex if index int ioctl join keys kill last lc lcfirst le length link listen local localtime log lstat
lt m mkdir msgctl msgget msgrcv msgsnd my ne next no not oct open opendir or ord pack package pipe pop print printf push q qq quotemeta qw qx rand read readdir readline
print EACH_FILE "#\!\/perl\n";
print EACH_FILE "# Made by $0 at: ", `date`, "\n";
print EACH_FILE $out_subs{$each_sub};
close EACH_FILE;
%out_subs=();
#chmod
}
}
}#""""""""""""" end of for (@file)
close LIB_FILE;
}else{
print OUT $_;
}
}
close OUT;
if($file =~/\.pl$/){ chmod 0755, $file; } # this makes it execu..
}
return(\@input_files); # returning the changed files
}
for $line(@lines){
$line=~s/$old//g;
print OUT $line;
}
close OUT;
if($file =~/\.pl$/){ chmod 0755, $file; } # this makes it execu..
}
}
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# --- MakeMaker tool_xsubpp section:
# --- MakeMaker tools_other section:
CHMOD = $(PERLRUN) -MExtUtils::Command -e chmod
CP = $(PERLRUN) -MExtUtils::Command -e cp
MV = $(PERLRUN) -MExtUtils::Command -e mv
NOOP = rem
NOECHO = @
RM_F = $(PERLRUN) -MExtUtils::Command -e rm_f
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check_type_and_open|5.009003||Viu
check_uni|5.003007||Viu
check_utf8|5.008000||Viu
check_utf8_print|5.013009||Viu
child_offset_bits|5.009003||Viu
chmod|5.005000||Viu
chsize|5.005000||Viu
ckDEAD|5.006000||Viu
ck_entersub_args_core|||iu
ck_entersub_args_list|5.013006|5.013006|
ck_entersub_args_proto|5.013006|5.013006|
KEY_break|5.027008||Viu
KEY_caller|5.003007||Viu
KEY_catch|5.033007||Viu
KEY_chdir|5.003007||Viu
KEY_CHECK|5.006000||Viu
KEY_chmod|5.003007||Viu
KEY_chomp|5.003007||Viu
KEY_chop|5.003007||Viu
KEY_chown|5.003007||Viu
KEY_chr|5.003007||Viu
KEY_chroot|5.003007||Viu
Perl_langinfo|5.027004|5.027004|n
PERL_LANGINFO_H|5.027004||Viu
PERL_LAST_5_18_0_INTERP_MEMBER|5.017009||Viu
Perl_ldexp|5.021003|5.021003|n
PerlLIO_access|5.005000||Viu
PerlLIO_chmod|5.005000||Viu
PerlLIO_chown|5.005000||Viu
PerlLIO_chsize|5.005000||Viu
PerlLIO_close|5.005000||Viu
PerlLIO_dup2|5.005000||Viu
PerlLIO_dup2_cloexec|5.027008||Viu
Perl_pp_aelemfast_lex|5.015000||Viu
Perl_pp_andassign|5.013009||Viu
Perl_pp_avalues|5.013009||Viu
Perl_pp_bind|5.013009||Viu
Perl_pp_bit_xor|5.013009||Viu
Perl_pp_chmod|5.013009||Viu
Perl_pp_chomp|5.013009||Viu
Perl_pp_connect|5.013009||Viu
Perl_pp_cos|5.013009||Viu
Perl_pp_custom|5.013009||Viu
Perl_pp_dbmclose|5.013009||Viu
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Makefile.old view on Meta::CPAN
# --- MakeMaker tool_xsubpp section:
# --- MakeMaker tools_other section:
SHELL = /bin/sh
CHMOD = chmod
CP = cp
MV = mv
NOOP = $(SHELL) -c true
NOECHO = @
RM_F = rm -f
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lib/Bot/Cobalt/Plugin/Auth.pm view on Meta::CPAN
return $authdb if try {
$serializer->writefile($authdb, $cloned);
my $p_cfg = plugin_cfg( $self );
my $perms = oct( $p_cfg->{Opts}->{AuthDB_Perms} // '0600' );
chmod($perms, $authdb);
1
};
logger->error("writefile() failure; $authdb $_");
return
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lib/Bot/Net/Script/Net.pm view on Meta::CPAN
my $dest_file = File::Spec->catfile($self->dist_name, 'bin', $script);
# Copy and make it executable
print "Copying in $dest_file...\n";
copy($source_file, $dest_file);
chmod 0555, $dest_file;
# If on a DOSish platform make bat file too
if (-e $source_file.'.bat') {
print "Copying in $dest_file.bat...\n";
copy($source_file.'.bat', $dest_file.'.bat');
chmod 0555, $dest_file.'.bat';
}
}
sub _write_makefile {
my $self = shift;
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lib/Brackup/Restore.pm view on Meta::CPAN
sub _update_statinfo {
my ($self, $full, $it) = @_;
push @{ $self->{_stats_to_run} }, sub {
if (defined $it->{Mode}) {
chmod(oct $it->{Mode}, $full) or
die "Failed to change mode of $full: $!";
}
if ($it->{Mtime} || $it->{Atime}) {
utime($it->{Atime} || $it->{Mtime},
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bryar-newblog view on Meta::CPAN
# These are defaults which are written out to be customized, so I don't
# feel bad about including them here inline.
# Blatant assumption of standard Unix
write_file("bryar.cgi", "#!/usr/bin/perl\nuse Bryar; Bryar->go()\n");
chmod 0755, "bryar.cgi";
write_file("bryar.conf",<<EOC);
name : My Bryar Weblog!
description : A blog without a more useful description
baseurl : http://where.will.i.be/
bryar-newblog view on Meta::CPAN
[% END %]
</tbody>
</table>
EOC
chmod 0644, $_ for ("bryar.conf", "1.txt", "head.html", "foot.html",
"template.html","template.rss", "template.atom",
"calendar.tt2", "blogmacros.tt2");
print "\nDone. Now you want to probably customize 'bryar.conf'.\n";
print "You should probably also customize template.html, head.html and foot.html\n";
print "Then point your browser at bryar.cgi, and get blogging!\n";
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Makefile.old view on Meta::CPAN
# --- MakeMaker tools_other section:
SHELL = /bin/sh
CHMOD = chmod
CP = cp
LD = cc
MV = mv
NOOP = $(SHELL) -c true
RM_F = rm -f
Makefile.old view on Meta::CPAN
POD2MAN_EXE = /tools/perl/5.005_03/bin/pod2man
POD2MAN = $(PERL) -we '%m=@ARGV;for (keys %m){' \
-e 'next if -e $$m{$$_} && -M $$m{$$_} < -M $$_ && -M $$m{$$_} < -M "Makefile";' \
-e 'print "Manifying $$m{$$_}\n";' \
-e 'system(qq[$$^X ].q["-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" $(POD2MAN_EXE) ].qq[$$_>$$m{$$_}])==0 or warn "Couldn\047t install $$m{$$_}\n";' \
-e 'chmod(oct($(PERM_RW))), $$m{$$_} or warn "chmod $(PERM_RW) $$m{$$_}: $$!\n";}'
manifypods : pure_all lib/Btrees.pm
@$(POD2MAN) \
lib/Btrees.pm \
$(INST_MAN3DIR)/Btrees.$(MAN3EXT)
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CPANReporter2.pm view on Meta::CPAN
Enter password/secret: zqxjkh
Writing profile to 'metabase_id.json'
$ mkdir ~/.cpanreporter
$ cp metabase_id.json ~/.cpanreporter/
$ chmod 400 ~/.cpanreporter/metabase_id.json
$ vi ~/.cpanreporter/config.ini
email_from = John Doe <jdoe@example.com>
transport = Metabase uri https://metabase.cpantesters.org/api/v1/ id_file ~/.cpanreporter/metabase_id.json
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CygwinVendor.pm view on Meta::CPAN
CPAN::Checksums 2.09
File::Remove 1.52
File::chmod 0.40
Params::Util 1.07
Test::Script 1.07
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Everything.pm view on Meta::CPAN
File::Which
File::Wildcard
File::chmod
File::lockf
FileHandle::Unget