dbolser’s gists

dbolser / gist:887272

Created March 25, 2011 17:55

	warn "connecting to link intensity GFF\n";

	my $intensities = Bio::DB::SeqFeature::Store->
	new( -adaptor => 'DBI::mysql',
	-dsn => 'dbolser_002:mysql.compbio.dundee.ac.uk',
	-user => 'dbolser',
	-pass => 'abc123',
	-verbose => $verbose,
	);

dbolser / gist:887301

Created March 25, 2011 18:12


	Line 1604 of /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
	print Dumper $self if !defined $source_tag; exit;


	Gives:

	$VAR1 = bless( {
	'dumpdir' => '/tmp',
	'settings_cache' => {

dbolser / gist:889192

Created March 27, 2011 13:03

asetaes

dbolser / gist:890433

Created March 28, 2011 13:21

	cpan[1]> install Bio::DB::BigWig
	CPAN: Storable loaded ok (v2.25)
	Going to read '/homes/dbolser/.cpan/Metadata'
	Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
	Running install for module 'Bio::DB::BigWig'
	Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
	CPAN: Digest::SHA loaded ok (v5.61)
	CPAN: Compress::Zlib loaded ok (v2.03)
	Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz ok
	CPAN: Archive::Tar loaded ok (v1.76)

dbolser / gist:890471

Created March 28, 2011 13:38

	cpan[1]> install Bio::DB::BigWig
	CPAN: Storable loaded ok (v2.25)
	Going to read '/homes/dbolser/.cpan/Metadata'
	Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
	Running install for module 'Bio::DB::BigWig'
	Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
	CPAN: Digest::SHA loaded ok (v5.61)
	CPAN: Compress::Zlib loaded ok (v2.03)
	Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz ok
	CPAN: Archive::Tar loaded ok (v1.76)

dbolser / gist:890472

Created March 28, 2011 13:38



	# autodetect if openssl is installed
	ifeq (${SSLDIR},)
	SSLDIR = /usr/include/openssl
	endif
	ifeq (${USE_SSL},)
	ifneq ($(wildcard ${SSLDIR}),)
	USE_SSL=1
	endif

dbolser / gist:890827

Created March 28, 2011 16:53

	[dbolser@cricket Bio-BigFile-1.05]$ ./perl Build.PL
	-bash: ./perl: No such file or directory
	[dbolser@cricket Bio-BigFile-1.05]$ perl Build.PL
	Created MYMETA.yml and MYMETA.json
	Creating new 'Build' script for 'Bio-BigFile' version '1.05'
	[dbolser@cricket Bio-BigFile-1.05]$ ./Build
	Building Bio-BigFile
	gcc -I/homes/dbolser/build/src/kent/src/inc -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
	lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigIntervalQuery’:
	lib/Bio/DB/BigFile.xs:172: warning: operation on ‘list’ may be undefined

dbolser / gist:891996

Created March 29, 2011 08:26

	CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz

	Created MYMETA.yml and MYMETA.json
	Creating new 'Build' script for 'Bio-BigFile' version '1.05'
	Building Bio-BigFile
	gcc -I/tmp/funk/kent/src/inc -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
	lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigIntervalQuery’:
	lib/Bio/DB/BigFile.xs:172: warning: operation on ‘list’ may be undefined
	lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummaryArray’:
	lib/Bio/DB/BigFile.xs:193: warning: operation on ‘values’ may be undefined

dbolser / gist:892034

Created March 29, 2011 08:59

	cp Parser/Encodings/x-sjis-jisx0221.enc blib/lib/XML/Parser/Encodings/x-sjis-jisx0221.enc
	cp Parser/Style/Stream.pm blib/lib/XML/Parser/Style/Stream.pm
	cp Parser/Encodings/iso-8859-5.enc blib/lib/XML/Parser/Encodings/iso-8859-5.enc
	make[1]: Entering directory `/homes/dbolser/.cpan/build/XML-Parser-2.40-piAYXa/Expat'
	cp Expat.pm ../blib/lib/XML/Parser/Expat.pm
	/usr/bin/perl /homes/dbolser/perl5/lib/perl5/ExtUtils/xsubpp -noprototypes -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap -typemap typemap Expat.xs > Expat.xsc && mv Expat.xsc Expat.c
	gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -DVERSION=\"2.40\" -DXS_VERSION=\"2.40\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" Expat.c
	Expat.xs: In function ‘gen

dbolser / gist:898133

Created April 1, 2011 13:25

	sub swapify {
	my $self = shift;

	## Take a copy
	my $swapped = $self->chimera;

	## Swap it
	$swapped->swap;

	## Return the swapified version

Dan B dbolser