jbrowse基因组浏览器部署

一、jbrowse部署

1.1 jbrowse部署

sudo mkdir /var/www/jbrowse;
sudo chown `whoami` /var/www/jbrowse;
# cd into it
cd /var/www/jbrowse;

1.2 nginx配置

  server {
        listen       80 default_server;
        listen       [::]:80 default_server;
        server_name  _;
        #root         /var/www/html/jbrowse;

        # Load configuration files for the default server block.
        include /etc/nginx/default.d/*.conf;

        location / {
        root  /var/www/html/jbrowse;
        autoindex on;
        index  index.html index.htm  index.jsp;
        }

        error_page 404 /404.html;
            location = /40x.html {
        }

fetch a JBrowse release zip file

curl -O http://jbrowse.org/releases/JBrowse-1.8.0.zip

# unzip it and cd into it
unzip JBrowse-1.8.0.zip
cd JBrowse-1.8.0

二 数据导入

1、 ca文件处理

samtools工具安装

 wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
  tar -jxvf samtools-1.9.tar.bz2 
  cd samtools-1.9/
  ./configure --prefix=/usr/local/samtools #编译
  make 
  make install

samtools faidx zdd0006.genome.v1.fa #生成ca文件的索引
执行命令后会自动生成文件zdd0006.genome.v1.fa.fai

2、vcf格式文件处理

确保你的 VCF 文件是经过 BGZF 压缩的（以 .vcf.gz 结尾），并且已经创建了相应的索引文件（.tbi 文件）。如果没有，你可以使用 bgzip 和 tabix 工具来进行压缩和索引。

tabix命令安装

git clone https://github.com/samtools/htslib.git
 git submodule update --init --recursive

然后进入项目make 和make install

数据处理

 bgzip -c 680_sample_filter_ID.vcf > 680_sample_filter_ID.vcf.gz
 tabix -p vcf 680_sample_filter_ID.vcf.gz

track.conf文件配置

[root@VM-4-17-opencloudos data]# cat tracks.conf 
[GENERAL]
refSeqs=Gmax_275_v2.0.fa.fai
[tracks.Gmax_275_v2.0]
urlTemplate=Gmax_275_v2.0.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence

refSeqs=SN14.genome.fa.fai
[tracks.SN14_genome]
urlTemplate=SN14.genome.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence

refSeqs=zdd0006.genome.v1.fa.fai
[tracks.zdd0006_genome]
urlTemplate=zdd0006.genome.v1.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence


[tracks.680_sample_filter]
# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate    = 680_sample_filter_ID.vcf.gz

 
# settings for how the track looks
category = VCF
type = JBrowse/View/Track/CanvasVariants
key  = 680_sample
#GFF格式
[tracks.Gmax_275_Wm82]
urlTemplate = Gmax_275_Wm82.a2.v1.gene.gff3
storeClass = JBrowse/Store/SeqFeature/GFF3
type = CanvasFeatures
key = Gmax_275_Wm82