User Tools

Site Tools


bigwiggbrowse

Utilisation des fichiers BigWig dans Gbrowse

sur debian

Prerequis: installer le package de kent et le compiler avec -fPIC
cd /usr/local/bioinfo/

wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

unzip jksrc.zip

cd kent/src

setenv MACHTYPE x86_64
apt-get install libmysqlclient-dev
apt-get install libmysqlclient16
setenv MYSQLLIBS /usr/lib/
setenv MYSQLINC /usr/include/mysql/
vi ./inc/common.mk pour modifier CFLAGS= en CFLAGS=-fPIC

#pour gbrowse on n'a besoin que des lib mais je conseille de compiler les outils, il y en a beaucoup (dont wigToBigWig)
make libs

#ce truc, c'est parce que le MACHTYPE que recupere le module perl n'est pas x86_64 donc le chemin qu'il cherchera sera lib//*.a
cp lib/x86_64/*.a lib 

Installation du module via cpan
apt-get install libssl-dev

cpan

install Bio::DB::BigWigSet


CPAN: File::Temp loaded ok (v0.22)

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.06.tar.gz


This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below. To prevent
this message from appearing in the future, set the environment variable KENT_SRC
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /usr/local/bioinfo/kent/src
Edition du fichier de configuration de gbrowse2 (certainement dans /etc/gbrowse2 )
[BigWig:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = -dir    '/home/gouzy/BigWigSet'

[BigWigIntervals]
feature  = summary
database = BigWig
glyph    = wiggle_xyplot
min_score = -80
max_score = 80
key       = RNAseq datasets
bgcolor   = darkblue

et maintenant il n'y a plus qu'a déposer les fichiers bigwig dans /home/gouzy/BigWigSet

bigwiggbrowse.txt · Last modified: 2011/08/02 16:14 by gouzy