Docker 中 GIVE 镜像的常用的命令

Docker 中 GIVE 镜像的常用的命令

此内容会随着时间的推移而不断改变

#--------------------------------------------
# 这是一个注释
# author：YKenan
# describe：GIVE
#--------------------------------------------
#############################################

## 进入 give container 的界面
docker exec -it give /bin/bash


## 创建 参考基因组 hg38
bash initial_ref.sh -u root -p Admin2015 -r hg38 -s "Homo sapiens" -c human  -f /tmp/example_data/cytoBandIdeo.txt -w '["chr10:30000000-50000000", "chr10:35000000-60000000"]'


## 在参考基因组上 添加 数据轨迹 "genes", "RNA_seq, "TAD", "genomic_interactions"
bash add_trackGroup.sh  -u root -p Admin2015 -r hg38 -g "genes" -l "Known Genes" -o 1 -s 0
bash add_trackGroup.sh  -u root -p Admin2015 -r hg38 -g "RNA_seq" -l "Gene Expression" -o 2 -s 0
bash add_trackGroup.sh  -u root -p Admin2015 -r hg38 -g "TAD" -l "Topologically Associating Domain" -o 3 -s 0
bash add_trackGroup.sh  -u root -p Admin2015 -r hg38 -g "genomic_interactions" -l "Genomic interactions from ChIA-PET" -o 3 -s 0


#----------------------
# 添加基因注释轨迹
#----------------------
#######################

## 自定义 文件
bash add_geneAnnot.sh  -u root -p Admin2015 -r hg38 -t "knownGene" -g "genes" -l "UCSC known genes annotation" -s "UCSC Genes" -o 1 -v full  -f /tmp/example_data/knownGene.txt


## .bed 文件
bash add_track_bed.sh -u root -p Admin2015 -r hg38 -t exampleBed -g "TAD" -l "An example bed track of TAD from HiC" -s "TAD" -o 2 -v pack -f /tmp/example_data/example.bed


## .bigWig 文件
bash add_track_bigWig.sh -u root -p Admin2015 -r hg38 -t exampleBW -g "RNA_seq" -l "An example bigWig from single cell RNAseq" -s "Gene Expression" -o 3 -v full -a true -f /tmp/example_data/example.bigWig


## .interaction 文件
bash add_track_interaction.sh -u root -p Admin2015 -r hg38 -t "exampleInteractions" -g "genomic_interactions" -l "An example genomic interactions from ChIA-PET data" -s "ChIA-PET Interactions" -o 1 -v full -q "0.37,1.32,1.78,2.19,2.60,2.97,3.43,3.85,4.34,4.90,5.48,6.16,6.94,8.01,9.05,10.41,12.37,14.88,19.84,31.77,290.17" -f /tmp/example_data/example.interaction


## 列出数据跟踪
bash list_tracks.sh -u root -p Admin2015 -r hg38


## 删除数据跟踪
bash remove_data.sh -u root -p Admin2015 -r hg38 -g TAD


## 删除 docker 中的 give 镜像中的域名
docker exec -t -i give /bin/bash
bash config_host.sh -r /var/www/give -d "http://give.genemo.org:40080"