install bioperl

How to install bioperl via cpan:

https://wiki.archlinux.org/index.php/Bioperl

bash>cpan

cpan>d /bioperl/

cpan>install xxx/bioperl-xxx.tar.gz

How to install GBrowse:

http://gmod.org/wiki/GBrowse_Install_HOWTO

bash>cpan -i CGI GD CGI::Session DBI DBD::mysql Digest::MD5 Text::Shellwords Class::BaseBio::GraphicsJSONCapture::TinyGD::SVG

>cpan -i DBD::SQLite or (depends on which you use)

>cpan -iDBD::mysql

optional:

>cpan -i Bio::DB::Das::Chado
>cpan -i XML::Parser XML::Writer XML::Twig XML::DOM LWP Bio::Das BioMOBY Math::FFT Statistics::Descriptive

After download http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.39/GBrowse-2.39.tar.gz/download

and tar zxf xxx.tar.gz,then cd xxx and run :

>perl Makefile.PL HTDOCS=/srv/http/tools/GBrowseCONF=/etc/conf.d/gbrowse CGIBIN=/srv/http/cgi-bin/

if some libs are missing,it will be shown,follow the tips.

>./Build test

>./Build install

>cd/etc/conf.d/gbrowse

>chmod +wGBrowse.conf

editGBrowse.conf:

tmp_base = /tmp/gbrowse2

url_base = /tools/GBrowse

db_base = /path/to/gbrowse2/database # where your database located

# add next line in [General] if you don't want generate pdf

generate pdf = 0

default source = yeast # a name for your sequence

add config for your sequence

[yeast]
description = Yeast chromosomes 1+2 (basic)
path = yeast_simple.conf # your sequence configuration file

edit yeast_simple.conf for your sequence

if you want to use sqlite: (There is a 'how to build sqlite database' in the bottom)

db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor 'DBI::SQLite'
-dsn '/path/to/your/sequence.sqlite'

How to build a sqlite database for gbrowse:

bp_seqfeature_load.pl -a DBI::SQLite -c -f -d name.db name.gff3 name.sca

How to load gff & fasta to postgresql database:

bp_seqfeature_load.pl -d 'dbi:Pg:dbname=yeast' -a DBI::Pg -c -u yeast -p 123456 yeast.gff3 yeast.fa

How to generate a gff3 file for sequence: simple example

cat convert_fasta2gff3.pl #!/usr/bin/perl -w use strict; use Bio::SeqIO; my ($file_fasta,$file_gff3)=@ARGV; die("$!: file_fasta file_gff3n")unless( $file_fasta && $file_gff3); open(F,'>',$file_gff3); my $in=Bio::SeqIO->new(-format=>'fasta',-file=>$file_fasta); while(my $s=$in->next_seq){ my $id=$s->id; my $seq=$s->seq; my ($seqid,$source,$type,$start,$end,$score,$strand,$phase,$attributes); $seqid=$id; $source="SOAPdenovo"; $type="WGS"; $start=1; $end=length($seq); $score='.'; $strand='.'; $phase='.'; $attributes="ID=$seqid;Name=$seqid;"; print F join("t",($seqid,$attributes)),"n"; } close(F);

（编辑：李大同）

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