CODEWITHSUNDEEP
centos6perl-modulegenomegoogle-genomicsjbrowse
onkar
onkar

Reputation: 39

alternative of jbrowse on centos

Is there an alternative Software of JBrowse (on Centos6).

I need to integrate one into my webpage, but jbrowse is giving error of zlib while installing PerlIO::gzip. Although all related modules (libpng,libpng-devel,gd-devel,zlib-devel,perl-ExtUtils-MakeMaker,Development Tools, perl-Compress-Zlib) are installed.

Any suggestion will be helpful. An alternative for windows8 os will also work.

Upvotes: 0

Views: 184

Answers (1)

Colin D
Colin D

Reputation: 3109

Note that there is a mailing list cross link for the JBrowse issue here here https://sourceforge.net/p/gmod/mailman/message/36349221/

Alternatives to JBrowse could include igv.js, pileup.js, genomeview, or other HTML5 genome browsers

Also note, if we take the stance that Perl pre-requisites really are impossible to install on your system, then we can take an alternative approach because JBrowse does not actually require Perl pre-requisites to be installed for operation. Modern JBrowse can load native file formats without using the Perl scripts for conversion.

In this case, you can simply create file directory like

data/genome.fa
data/genome.fa.fai
data/tracks.conf
data/annotations.sorted.gff.gz
data/annotations.sorted.gff.gz.tbi

where genome.fa.fai is generated by samtools faidx genome.fa and annotations.sorted.gff.gz is generated by sort -k1,1 -k4,4n annotations.gff > annotations.sorted.gff and then bgzip annotations.sorted.gff.gz and finally tabix -p vcf annotations.sorted.gff.gz

Then the tracks.conf file can contain

[GENERAL]
refSeqs=genome.fa.fai

[tracks.refseq]
urlTemplate=genome.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence
[tracks.annotations]
urlTemplate=annotations.sorted.gz
type=CanvasFeatures
storeClass=JBrowse/Store/SeqFeature/GFF3Tabix

In this sense, your browser can be fully created without perl pre-requisites

Upvotes: 0

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