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JBrowse - client-side genome browser
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Sample configuration bash script</h1></header><article><div><span><p>A common way of preparing data for usage in JBrowse is running the perl pre-processing scripts. These are not CGI perl scripts, they simple transform some feature data into JSON format for JBrowse to statically consume.</p>
<p>Here is an example script that prepares an instance of tomato genomic data</p>
<pre><code class="hljs">#!/usr/bin/env bash
## example script that fetches and formats large data from the tomato
## genome (similar in size to Human) using flatfile-to-json
IN='sample_data/raw/tomato';
OUT='sample_data/json/tomato';
# uncomment the line below to compress all the datasets on disk
# (requires a little bit of web server configuration for the files to
# be served correctly)
#COMPRESS='--compress'
set -e;
rm -rf $OUT;
mkdir -p $IN $OUT;
# fetch the tomato data using `wget` (about 1G total)
for f in ITAG2.3_assembly.gff3 \
ITAG2.3_gene_models.gff3 \
ITAG2.3_genomic.fasta \
ITAG2.3_cdna_alignments.gff3 \
ITAG2.3_sgn_data.gff3 \
; do
if [ ! -e $IN/$f ]; then
wget -v -O $IN/$f ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.3_release/$f;
fi
done
set -x;
# format the reference sequences
bin/prepare-refseqs.pl $COMPRESS --fasta $IN/ITAG2.3_genomic.fasta --out $OUT;
# official ITAG2.3 gene models
bin/flatfile-to-json.pl $COMPRESS \
-<span class="ruby">-out $OUT \
</span> -<span class="ruby">-gff $IN/ITAG2.<span class="hljs-number">3_</span>gene_models.gff3 \
</span> -<span class="ruby">-type mRNA \
</span> -<span class="ruby">-autocomplete all \
</span> -<span class="ruby">-trackLabel genes \
</span> -<span class="ruby">-key <span class="hljs-string">'Gene models'</span> \
</span> -<span class="ruby">-getSubfeatures \
</span> -<span class="ruby">-className transcript \
</span> -<span class="ruby">-subfeatureClasses <span class="hljs-string">'{"CDS": "transcript-CDS", "exon": "hidden"}'</span> \
</span> -<span class="ruby">-arrowheadClass arrowhead \
</span> -<span class="ruby">-urltemplate <span class="hljs-string">"http://solgenomics.net/search/quick?term={name}"</span> \
</span> ;
# SL2.40 assembly
bin/flatfile-to-json.pl $COMPRESS \
-<span class="ruby">-out $OUT \
</span> -<span class="ruby">-trackLabel assembly \
</span> -<span class="ruby">-key <span class="hljs-string">'Assembly'</span> \
</span> -<span class="ruby">-gff $IN/ITAG2.<span class="hljs-number">3_</span>assembly.gff3 \
</span> -<span class="ruby">-type supercontig,remark \
</span> -<span class="ruby">-autocomplete all \
</span> -<span class="ruby">-getSubfeatures \
</span> -<span class="ruby">-className generic_parent \
</span> -<span class="ruby">-subfeatureClasses <span class="hljs-string">'{"contig": "feature3"}'</span> \
</span> -<span class="ruby">-urltemplate <span class="hljs-string">"http://solgenomics.net/search/quick?term={name}"</span> \
</span> ;
# SGN unigene alignments
bin/flatfile-to-json.pl $COMPRESS \
-<span class="ruby">-out $OUT \
</span> -<span class="ruby">-trackLabel sgn_unigenes \
</span> -<span class="ruby">-key <span class="hljs-string">'SGN unigenes'</span> \
</span> -<span class="ruby">-gff $IN/ITAG2.<span class="hljs-number">3_</span>sgn_data.gff3 \
</span> -<span class="ruby">-type <span class="hljs-symbol">match:</span>ITAG_sgn_unigenes \
</span> -<span class="ruby">-autocomplete all \
</span> -<span class="ruby">-getSubfeatures \
</span> -<span class="ruby">-className generic_parent \
</span> -<span class="ruby">-subfeatureClasses <span class="hljs-string">'{"match_part": "match_part"}'</span> \
</span> -<span class="ruby">-arrowheadClass <span class="hljs-string">'arrowhead'</span> \
</span> -<span class="ruby">-urltemplate <span class="hljs-string">"http://solgenomics.net/search/quick?term={name}"</span> \
</span> ;
# microtom cDNA alignments
bin/flatfile-to-json.pl $COMPRESS \
-<span class="ruby">-out $OUT \
</span> -<span class="ruby">-trackLabel microtom_cdna \
</span> -<span class="ruby">-key <span class="hljs-string">'MicroTom full-length cDNAs'</span> \
</span> -<span class="ruby">-gff $IN/ITAG2.<span class="hljs-number">3_</span>cdna_alignments.gff3 \
</span> -<span class="ruby">-type <span class="hljs-symbol">match:</span>ITAG_microtom_flcdnas \
</span> -<span class="ruby">-autocomplete all \
</span> -<span class="ruby">-getSubfeatures \
</span> -<span class="ruby">-className generic_parent \
</span> -<span class="ruby">-subfeatureClasses <span class="hljs-string">'{"match_part": "match_part"}'</span> \
</span> -<span class="ruby">-arrowheadClass <span class="hljs-string">'arrowhead'</span> \
</span> ;
# SGN marker sequences
bin/flatfile-to-json.pl $COMPRESS \
-<span class="ruby">-out $OUT \
</span> -<span class="ruby">-trackLabel sgn_markers \
</span> -<span class="ruby">-key <span class="hljs-string">'SGN markers'</span> \
</span> -<span class="ruby">-gff $IN/ITAG2.<span class="hljs-number">3_</span>sgn_data.gff3 \
</span> -<span class="ruby">-type <span class="hljs-symbol">match:</span>ITAG_sgn_markers \
</span> -<span class="ruby">-autocomplete all \
</span> -<span class="ruby">-getSubfeatures \
</span> -<span class="ruby">-className transcript \
</span> -<span class="ruby">-subfeatureClasses <span class="hljs-string">'{"match_part": "match_part"}'</span> \
</span> -<span class="ruby">-arrowheadClass <span class="hljs-string">'arrowhead'</span> \
</span> -<span class="ruby">-urltemplate <span class="hljs-string">"http://solgenomics.net/search/quick?term={name}"</span> \
</span> ;
# index feature names
bin/generate-names.pl --out $OUT;
echo "To see the formatted ITAG2.3 tomato genome, point your browser at http://your.jbrowse.root/index.html?data=sample_data/json/tomato";
</code></pre>
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