By chenyi, 23 April, 2024
Forums

1、在网页端的module中打开jbrowse的模块,Tripal JBrowse ManagementTripal-JBrowse Page Integration

 

2、在tripal/Extensions/Tripal JBrowse Management网页下,右上角的setting中配置jibrowse

    注意data directory会报错显示jbrowse不可写,要回到服务器端对jbrowse权限进行改写 chmod 777 jbrowse

 

3、在服务器端的/var/www/html/sites/default/files/jbrowse中创建对应的物种文件夹 Torreya_grandis,在Torreya_grandis中使用以下两个命令来处理数据

 

/var/www/html/tools/JBrowse/bin/prepare-refseqs.pl --fasta ../../raw/Torreya_grandis/Tgra.cds.fa

 

/var/www/html/tools/JBrowse/bin/flatfile-to-json.pl --gff ../../raw/Torreya_grandis/Tgra.chr.gff --trackType CanvasFeatures --trackLabel gff

 

4 将创建好的数据挂载到网页端。在网页端中通过Home / Administration / Tripal / Extensions / Tripal JBrowse Management中点击Register Existing Instance

填写好OrganismSequence Assembly