igvR 1.14.0
吉姆·罗宾逊和他的团队目前提供的16个参考基因组:
每个包括部分或全部:
你指定参考基因组的兴趣igvR是这样的:
igv < - igvR () setGenome(进口,“hg38”)如果你想使用一个参考基因组以外,我们提供一种方法setCustomGenome。下面是一个示例调用股票hg38参考基因组的显式地指定。这可能被视为冗余,但依赖的美德值得信任地可用的参考文件。
见下面的进一步指出在一个可能的方法来服务你的文件如果您需要这样做你自己。
igv < - igvR () setCustomGenome (igv id =“hg38 genomeName =“人类(GRCh38 / hg38)”fastaURL = " https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa ", fastaIndexURL = " https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai ", chromosomeAliasURL = NA, cytobandURL = " https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt ", geneAnnotationName =“Refseq基因”,geneAnnotationURL = " https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz ", geneAnnotationTrackHeight = 300, geneAnnotationTrackColor =暗绿色,initialLocus =“chr5:88,621,308 - 89001037”, visibilityWindow = 5000000)许多这个方法的参数默认为NA。这是一个极简主义者调用:
setCustomGenome (igv id =“hg38 genomeName =“人类(GRCh38 / hg38)”fastaURL = " https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa ", fastaIndexURL = " https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai ")任何进口。js-compatible web服务器必须有两个功能:
我用一个容易安装,轻松配置Python瓶网络服务器。这里有详细的安排,
从进口瓶瓶flask_cors进口歌珥应用=瓶(__name__ static_url_path = /静态)歌珥(app) @app.route (“/”) def serveStaticFiles():返回的歌珥和字节范围请求烧瓶网络服务器igvR和igvShiny if __name__ = =“__main__”: app.run(主机= 0.0.0.0,端口= ' 60050 ')
把文件你希望在,例如,http://locahhost: 60050 /静态/。python运行网络服务器:
bash >出口FLASK_APP = serveStaticGenomeFiles。py bash > nohup瓶运行- p 60050——主机= 0.0.0.0 & >烧瓶。日志和
从python serveStaticGenomeFiles副本。py / app /复制的要求。txt / app / WORKDIR /应用程序运行pip安装- r的要求。txt入口点(“python”) CMD (“serveStaticGenomeFiles.py”)
瓶flask_cors
构建:码头工人建造- t flask-cors-server:最新。运行:码头工人跑——\ - p 5000:60050 \ - v ~ / /码头工人/瓶/ web /例子:/ app \ flask-cors-server站:码头工人停止的码头工人ps | grep flask-cors-webserver | awk的{打印1美元}' '