docker学习笔记

基础镜像仅包含：R,java,python2 and python3
https://hub.docker.com/r/fanyucai1/base

生信肿瘤变异检测的软件环境
++++++++++++++++++++++++++++++++
https://hub.docker.com/r/fanyucai1/bio_tumor

软件列表如下：

software_list

annovar

/software/annovar/annotate_variation.pl
/software/annovar/table_annovar.pl
/software/annovar/convert2annovar.pl
/software/annovar/retrieve_seq_from_fasta.pl
/software/annovar/coding_change.pl
/software/annovar/variants_reduction.pl

msisensor(v0.6)

/software/MSIsensor/msisensor-0.6/msisensor

msisensor2(v0.1,https://github.com/niu-lab/msisensor2)

/software/msisensor2/msisensor2-master/msisensor2
/software/msisensor2/msisensor2-master/models_hg19_GRCh37
/software/msisensor2/msisensor2-master/models_hg38

bcl2fastq(v2.20.0.422)

/software/bcl2fastq/bcl2fastq/bin/bcl2fastq

cnvkit

/software/CNVkit/data/access-5k-mappable.hg19.bed
/software/CNVkit/data/refFlat.txt

pindel(Pindel version 0.2.5b8)

  /software/Pindel/pindel

htslib(1.9)

/software/htslib/tabix

bwa(0.7.17)

/software/bwa/bwa-0.7.17/bwa

gatk(4.1.3.0)

/software/GATK/gatk-4.1.3.0/gatk

gatk(3.7)

/software/GATK/3.7/GenomeAnalysisTK.jar

bedtools(2.28.0)

 /software/bedtools/bedtools2/bin/bedtools

fastp(version 0.20.0)

/software/fastp/fastp

genefuse(v0.6.1)

/software/genefuse/genefuse
/software/genefuse/genes/cancer.hg19.csv
/software/genefuse/genes/druggable.hg19.csv

bcftools

/software/bcftools/bcftools-v1.9/bin/bcftools

picard(2.20.6)

/software/picard/picard.jar

fgbio(1.0.0)

 /software/fgbio/fgbio-1.0.0.jar

vardict(1.6.0)

/software/vardict/VarDict-1.6.0/bin/VarDict

delly(v0.8.1)

/software/Delly/delly_v0.8.1_linux_x86_64bit
/software/Delly/human.hg19.excl.tsv

samtools(1.9)

/software/samtools/samtools-v1.9/bin/samtools

Trimmomatic(0.39)

/software/Trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar

abra2(2.20)

/software/abra2/abra2-2.20.jar

R(v3.6)

/usr/bin/R

java(v1.8.0_222)

/usr/bin/java

python2(2.7.5)

/usr/bin/python:
/usr/bin/pip2
    CNVkit-0.9.6 
    HTSeq-0.11.2 
    MySQL-python-1.2.5 
    PyVCF-0.6.8 
    PyYAML-5.1.2 
    RSeQC-2.6.6 
    backports-abc-0.5 
    backports.functools-lru-cache-1.5 
    biopython-1.74 
    bx-python-0.8.4 
    bz2file-0.98 
    click-7.0 
    configparser-3.8.1 
    cutadapt-1.16 
    cycler-0.10.0 
    decorator-4.4.0 
    future-0.17.1 
    futures-3.3.0 
    joblib-0.13.2 
    json5-0.8.5 
    kiwisolver-1.1.0 
    matplotlib-2.2.2 
    networkx-2.2 
    numpy-1.14.4 
    pandas-0.23.2 
    parse-1.12.1 
    parse2csv-0.1.4 
    pillow-6.1.0 
    pomegranate-0.11.1 
    pyfaidx-0.5.5.2 
    pyparsing-2.4.2 
    pysam-0.15.1 
    pysqlite-2.8.3 
    python-dateutil-2.8.0 
    pytz-2019.2 
    reportlab-3.5.23 
    scikit-learn-0.20.0 
    scipy-1.2.0 
    seaborn-0.8 
    singledispatch-3.4.0.3 
    six-1.12.0 
    subprocess32-3.5.4 
    tornado-5.1.1 
    wheel-0.33.6 
    xopen-0.8.1

python3(v3.7.0)

/software/python3/Python-v3.7.0/bin/python3
/software/python3/Python-v3.7.0/bin/pip3
     CNVkit-0.9.6 
     PyVCF-0.6.8 
     PyYAML-5.1.2 
     RSeQC-3.0.0 
     bx-python-0.8.4 
     click-7.0 
     cutadapt-2.4 
     decorator-4.4.0 
     dnaio-0.3 
     edlib-1.3.4 
     future-0.17.1 
     joblib-0.13.2 
     networkx-2.3 
     parse-1.12.1 
     parse2csv-0.1.4 
     pillow-6.1.0 
     pomegranate-0.11.1 
     pyBigWig-0.3.17 
     pyfaidx-0.5.5.2 
     reportlab-3.5.23 
     scikit-learn-0.21.3 
     scipy-1.3.1 
     seaborn-0.9.0 
     tornado-6.0.3 
     wheel-0.33.6 
     xopen-0.8.1
     scp-0.13.2
     twilio-6.34.0
     multiprocess-0.70.9
     requests-2.22.0
     pathos-0.2.5
     paramiko-2.7.0
     demjson-2.2.4

常规docker 命令：

	FROM ubuntu:18.04
    ENV LC_ALL="C.UTF-8"
    ENV LANG="C.UTF-8"
    ENV DEBIAN_FRONTEND noninteractive
    ENV DEBCONF_NONINTERACTIVE_SEEN true
    RUN mkdir -p /project/
    WORKDIR /project/
    ENV PATH /opt/conda/bin:$PATH
    COPY hisat2-2.1.0-Linux_x86_64.zip ./
    RUN unzip hisat2-2.1.0-Linux_x86_64.zip && ln -s hisat2-2.1.0 bin/

	docker build -t hisat2:2.1.0 .
    docker rm $(docker ps -a -q) 删除所有容器
    docker rmi -f 删除镜像
    docker save -o ubuntu_haha.tar ubuntu:latest
    docker load --input ubuntu_haha.tar

	当docker遇到image has dependent child images
    ####    停止所有容器
    docker ps -a | grep "Exited" | awk '{print $1 }'|xargs docker stop
    ####    删除所有容器
    docker ps -a | grep "Exited" | awk '{print $1 }'|xargs docker rm
    ####    删除所有none镜像
    docker images|grep none|awk '{print $3 }'|xargs docker rmi
    ####    强制删除镜像
    docker rmi -f 8f5116cbc201
    ####    停止正在运行的容器
    docker stop 3e42fb38f847