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JBrowse FAQ

GMOD.org recent changes - Sat, 07/21/2018 - 11:51

‎How do I create a Tabix indexed GFF

← Older revision Revision as of 15:51, 21 July 2018 (One intermediate revision by the same user not shown)Line 223: Line 223:  Then move that directory into your web server root and you are ready to go. Then move that directory into your web server root and you are ready to go.    −Note: If you want to make your own custom build with minification (which reduces HTTP load on your users), you can install "cpanm Text::Markdown" and "cpanm DateTime" and then run the jbrowse Makefile+Note: If you want to make your own custom build you can use    − make -f build/Makefile release-notest     −This purposefully excludes the perl test suite, but you can run those too with+ make -f build/Makefile release       − make -f build/Makefile release+Also also note: post 1.13.0 releases of JBrowse will automatically create a minified custom build when you run ./setup.sh if you have a -dev release or a github clone.     == What are the different config file formats? == == What are the different config file formats? == Line 694: Line 693:     Note that you can try and use GNU sort (sort -k1,1 -k4,4n) or genometools (gt gff3 -sortlines) but these both have problems where it will place child features behind the parent features in the GFF Note that you can try and use GNU sort (sort -k1,1 -k4,4n) or genometools (gt gff3 -sortlines) but these both have problems where it will place child features behind the parent features in the GFF  +  +In JBrowse 1.14, the problem of child features being behind their parents was fixed so the full GFF3Sort algorithm from @billzt is now not necessary and a simple GNU sort does work.     == How do I create a Indexed FASTA? == == How do I create a Indexed FASTA? == Colin Diesh
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