cjfields

UID                 :57147
Name                :SCYL3
Description         :SCY1-like 3 (S. cerevisiae)
Orgname             :Homo sapiens
Status              
CurrentID           
Chromosome          :1
GeneticSource       :genomic
MapLocation         :1q24.2
OtherAliases        :PACE-1, PACE1, RP1-97P20.2

cjfields

#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::EUtilities;
 
# this needs to be a list of EntrezGene unique IDs
my @ids   = @ARGV;
 
my $eutil   = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                       -email => 'mymail@foo.bar',

cjfields

---
abstract: 'BioPerl-Network - package for biological networks'
author:
  - 'BioPerl Team <bioperl-l@bioperl.org>'
build_requires: {}
configure_requires:
  Module::Build: 0.38
dynamic_config: 1
generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.110440'
license: perl

cjfields

t/Align/AlignStats.t ......................... ok
t/Align/AlignUtil.t .......................... ok
t/Align/Graphics.t ........................... ok
t/Align/SimpleAlign.t ........................ ok
t/Align/TreeBuild.t .......................... ok
t/Align/Utilities.t .......................... ok
t/AlignIO/AlignIO.t .......................... ok
t/AlignIO/arp.t .............................. ok
t/AlignIO/bl2seq.t ........................... ok
t/AlignIO/clustalw.t ......................... ok

cjfields

[cjfields@portal extensions]$ ll
total 64
lrwxrwxrwx  1 apache apache  65 Nov 20  2009 analytics.php -> /home/websites/cross-site-stuff/mediaWikiExtentions/analytics.php
lrwxrwxrwx  1 apache apache  62 Nov 20  2009 Biblio.php -> /home/websites/cross-site-stuff/mediaWikiExtentions/Biblio.php
lrwxrwxrwx  1 root   root    52 Mar  7 17:09 CheckUser -> /home/websites/cross-site-stuff/extensions/CheckUser
lrwxrwxrwx  1 root   root    63 Feb  8 20:14 ConfirmEdit -> /home/websites/cross-site-stuff/mediaWikiExtentions/ConfirmEdit
lrwxrwxrwx  1 apache apache  57 Nov 19  2009 geshi -> /home/websites/cross-site-stuff/mediaWikiExtentions/geshi
lrwxrwxrwx  1 apache apache  70 Nov 20  2009 GeSHiHighlight.php -> /home/websites/cross-site-stuff/mediaWikiExtentions/GeSHiHighlight.php
lrwxrwxrwx  1 apache apache  61 Nov 20  2009 geshi.php -> /home/websites/cross-site-stuff/mediaWikiExtentions/geshi.php
lrwxrwxrwx  1 apache apache  58 Nov 19  2009 googleAnalytics -> /home/websites/cross-site-stuff/extensions/googleAnalytics

cjfields

require_once("$IP/extensions/OpenID/OpenID.setup.php");
$wgTrustRoot = "http://www.bioperl.org";
$wgOpenIDShowProviderIcons = true;

cjfields

---
abstract: 'BioPerl-DB - package for biological databases'
author:
  - 'BioPerl Team <bioperl-l@bioperl.org>'
build_requires: {}
configure_requires:
  Module::Build: 0.38
dynamic_config: 1
generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.110580'
license: perl

cjfields

All,

Lincoln needs a new BioPerl release to CPAN ASAP to coordinate with the latest
GBrowse2 release. The latest GBrowse2 requires v BioPerl 1.0069, which is what
we're using on the master branch to distinguish from the 1.6 branch version (the
master branch version meant to designate 'just prior to 1.7'). However, we were
planning on designating the next release as 1.6.2 (or, 1.006002), which will not
match with GBrowse's requirements.

Instead of asking Lincoln to change GBrowse to reflect that, and b/c this

cjfields

....

Do you want to run tests requiring a valid email address? y/n [n] y
Enter email address:  cjfields@bioperl.org
Could not get valid metadata. Error is: Invalid metadata structure. Errors:
'Perl_5' for 'license' does not have a URL scheme (resources -> license)
[Validation: 1.2], Expected a map structure from string or file.
(optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2],
Expected a map structure from string or file. (optional_features ->
Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from

cjfields

cjfields@pyrimidine:~/tests/seq$ cat locations_bm.pl 
#!/usr/bin/perl -w

use Modern::Perl;
use Bio::SeqIO;
use Benchmark qw(cmpthese);

my $file = shift;

cmpthese(10, {