Gbrowse在windows安装.docx

Gbrowse在windows安装一、 准备工作ActivePerl /Products/Download/Download.plex?id=ActivePerlApache /download.cgi （可下最新版本）MySQL /downloads/mysql （可下最新版本）gbrowse_netinstall.pl （在线安装perl脚本，需要perl环境）/viewvc/gmod/Generic-Genome-Browser/trunk/bin/gbrowse_netinstall.pl 注：ActivePerl 需要下version 5.8.XX版，其它版本暂不支持二、 安装ActivePerlApacheMysql(可先不安) gbrowse_netinstall.pl (cmd窗口调用,命令：perl gbrowse_netinstall.pl)注：运行过程中可能会出现下列错误： “ Couldnt install nmake.exe. No such file such file or directory at gbrowse_netinstall.pl line 150. Begin failed-Compilation aborted at gbrowse_netinstall.pl line 158”解决办法：出现上错误时，可选择手动将150行“#”注释掉，重新运行即可！安装后可以正常使用。安装过程需要根据网速，大概半小时左右！三、 调试安装完毕浏览器出现下界面表示初步成功！如果点击example database 下面的链接能正常显示（恭喜你，成功了）通常是如下显示，不正常显示：示例如下图：问题解决：修改C:Program FilesApache Software FoundationApache2.2cgi-bin 目录下“gbrowse”文件，将“#!C:/Perl/bin/perl.exe -w”“$CONF_DIR = C:/Program Files/Apache Software Foundation/Apache2.2/conf/gbrowse.conf;”中的“”做替换即可。调试完毕后，单击“http:/localhost/cgi-bin/gbrowse/yeast”测试1. ced with the %09 URL escape. 文件目录及程序运行说明下文目录结构均在activeperl 、apache 在默认情况下安装程序运行需准备文件及文件所在目录：C:Program FilesApache Software FoundationApache2.2confgbrowse.conf 目录下：XXXX.conf 配置文件 通过配置文件到相应目录取数据库。C:Program FilesApache Software FoundationApache2.2htdocsgbrowsedatabases 目录下取数据文件程序尝试使用简记：l Gbrowse 页面展示文件相关文件目录：C:Program FilesApache Software FoundationApache2.2htdocs/gbrowsel Gbrowse配置文件C:Program FilesApache Software FoundationApache2.2conf/gbrowse.confl GBrowse CGI (web) scripts C:Program FilesApache Software FoundationApache2.2cgi-bin/gbrowse C:Program FilesApache Software FoundationApache2.2cgi-bin/gbrowse_img C:Program FilesApache Software FoundationApache2.2cgi-bin/gbrowse_details C:Program FilesApache Software FoundationApache2.2cgi-bin/gbrowse_est C:Program FilesApache Software FoundationApache2.2cgi-bin/gbrowse_syn C:Program FilesApache Software FoundationApache2.2cgi-bin/gbrowse_moby 注：当前版本数据格式.gff3，.gff不支持 ；支持格式如下：#gff-version 3#Note: See # file: volvox1.gff3ctgAexamplecontig150000.Name=ctgActgAexampleremark16591984.+.Name=f07;Note=This is an examplectgAexampleremark30146130.+.Name=f06;Note=This is another examplectgAexampleremark47155968.-.Name=f05;Note=Ok! Ok! I get the message.ctgAexampleremark1328016394.+.Name=f08ctgAexampleremark1532915533.+.Name=f10ctgAexampleremark1915722915.-.Name=f13ctgAexampleremark2213224633.+.Name=f15ctgAexampleremark2307223185.+.Name=f14ctgAexampleremark2456228338.+.Name=f02ctgAexampleremark3603438167.+.Name=f09ctgAexampleremark3664940440.-.Name=f03ctgAexampleremark3724238653.+.Name=f04ctgAexampleremark4470547713.-.Name=f01ctgAexampleremark4699048410.-.Name=f11ctgAexampleremark4975850000.-.Name=f12数据格式简单描述：数据9列，缺失项“.”代替详细参考：/resources/gff3.htmlGFF3文件注释说明：1. reference sequenceThis is the name of the feature that will be used to establish the coordinate system for the annotation. This is usually the name of a chromosome, a clone, or a contig. In our example, the reference sequence is ctgA. A single GFF file can refer to multiple reference sequences.2. sourceThe source of the annotation. This field describes how the feature was derived. In the example, the source is example for want of a better description. Many people find the source as a way of distinguishing between similar features that were derived by different methods, for example, gene calls derived from different prediction software. You can leave this column blank by replacing the source with a single dot (.).3. typeThis column describes the feature type. Although, you can choose anything you like to describe the feature type, you are strongly encouraged to use well-recognized sequence ontology (SO) terms such as gene, repeat_region, exon, and CDS. You can find a list of the recognized SO terms at the Sequence Ontology Project web site. For lack of a better name, the features in the volvox example are of type remark. Another 4. start positionThe position that the feature starts at, relative to the reference sequence. The first base of the reference sequence is position 1.5. end positionThe end of the feature, again relative to the reference sequence. End is always greater than or equal to start.6. scoreFor features that have a numeric score, such as sequence similarities, this field holds the score. Score units are arbitrary, but most people use the expectation value for similarity features. You can leave it blank by replacing the column with a dot.7. strandFor features that are strand-specific, this field is the strand on which the annotation resides. It is + for the forward strand, - for the reverse strand, or . for annotations that are not stranded. If you are unsure of whether a feature is stranded, it wont hurt to use a + here.8. phaseFor CDS features that encode proteins, this field describes where the next codon starts. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature in order to reach the first base of the next codon. In other words, a phase of 0 indicates that the next codon begins at the first base of the region described by the current line, a phase of 1 indicates that the next codon begins at the second base of this region, and a phase of 2 indicates that the next codon begins at the third base of this region. This information is used by the cds glyph to show how the reading frame changes across splice sites. For all other feature types, use a dot here.attributesA list of feature attributes in the format tag=value. Multiple tag=value pairs are separated by semicolons. URL escaping rules are used for tags or values containing the following characters: ,=;. Spaces are allowed in this field, but tabs must be repla数据运行文件准备：数据库文件C:Program FilesApache Software FoundationApache2.2htdocsgbrowsedatabases配置文件：C:Program FilesApache Software FoundationApache2.2conf/gbrowse.conf配置文件说明：ExampleFeaturesfeature = remarkglyph = genericstranded = 1bgcolor = blueheight = 10key = Example Featuresfeatureoption indicates what feature type(s) to display inside the track. glyph option specifies the shape of the rendered feature. The default is generic, which is a simple filled box, but there are dozens of glyphs to choose from.（形状控制） stranded option tells the generic glyph to try to display the strandedn