CODEWITHSUNDEEP
dockerdocker-compose
mpiot
mpiot

Reputation: 1522

Wget in Dockerfile, files disappear in container

In a Docker file I use wget to download file in the image. But when I use this image in a docker-compose file, the container doesn't contains the files...

    FROM debian:8

    RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*

    RUN mkdir -p /blast  && cd /blast
    RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.6.0+-x64-linux.tar.gz
    RUN tar zxvpf ncbi-blast-2.6.0+-x64-linux.tar.gz && rm ncbi-blast-2.6.0+-x64-linux.tar.gz
    RUN export PATH=$PATH:/blast/ncbi-blast-2.6.0+/bin
    #&& export BLASTDB=/blast/blastdb

    CMD ["sleep", "infinity"]

In the container I've the /blast folder, but not the files... Someon know how I can do a wget and keep files ? And why they disappear ?

EDIT

The docker history

    IMAGE               CREATED             CREATED BY                                      SIZE                COMMENT
    13361cc1dda8        9 minutes ago       /bin/sh -c #(nop)  CMD ["sleep" "infinity"]     0 B                 
    748afb9b0a0a        9 minutes ago       /bin/sh -c #(nop) WORKDIR /blast                0 B                 
    6eb2b58af7d4        9 minutes ago       /bin/sh -c export PATH=$PATH:/blast/ncbi-b...   0 B                 
    1331a22dcf67        10 minutes ago      /bin/sh -c wget ftp://ftp.ncbi.nlm.nih.gov...   675 MB              
    83d2844843e5        35 minutes ago      /bin/sh -c mkdir -p /blast  && cd /blast        0 B                 
    6b0b6a13ae47        41 minutes ago      /bin/sh -c apt-get update && apt-get insta...   41.2 MB             
    054abe38b1e6        12 hours ago        /bin/sh -c #(nop)  CMD ["/bin/bash"]            0 B                 
    <missing>           12 hours ago        /bin/sh -c #(nop) ADD file:712c48086043553...   123 MB

The output of docker-compose build (extract part)

    2017-04-25 07:41:47 (10.1 MB/s) - 'ncbi-blast-2.6.0+-x64-linux.tar.gz' saved [222504398]

    ncbi-blast-2.6.0+/
    ncbi-blast-2.6.0+/ChangeLog
    ncbi-blast-2.6.0+/LICENSE
    ncbi-blast-2.6.0+/ncbi_package_info
    ncbi-blast-2.6.0+/doc/
    ncbi-blast-2.6.0+/doc/README.txt
    ncbi-blast-2.6.0+/bin/
    ncbi-blast-2.6.0+/bin/makeblastdb
    ncbi-blast-2.6.0+/bin/tblastx
    ncbi-blast-2.6.0+/bin/tblastn
    ncbi-blast-2.6.0+/bin/blastn
    ncbi-blast-2.6.0+/bin/blastdb_aliastool
    ncbi-blast-2.6.0+/bin/update_blastdb.pl
    ncbi-blast-2.6.0+/bin/windowmasker
    ncbi-blast-2.6.0+/bin/psiblast
    ncbi-blast-2.6.0+/bin/blastx
    ncbi-blast-2.6.0+/bin/rpsblast
    ncbi-blast-2.6.0+/bin/segmasker
    ncbi-blast-2.6.0+/bin/blastdbcheck
    ncbi-blast-2.6.0+/bin/rpstblastn
    ncbi-blast-2.6.0+/bin/deltablast
    ncbi-blast-2.6.0+/bin/makembindex
    ncbi-blast-2.6.0+/bin/convert2blastmask
    ncbi-blast-2.6.0+/bin/blastp
    ncbi-blast-2.6.0+/bin/dustmasker
    ncbi-blast-2.6.0+/bin/makeprofiledb
    ncbi-blast-2.6.0+/bin/blastdbcmd
    ncbi-blast-2.6.0+/bin/legacy_blast.pl
    ncbi-blast-2.6.0+/bin/blast_formatter
    ncbi-blast-2.6.0+/README
     ---> 1331a22dcf67
    Removing intermediate container 06070bb79e70

Upvotes: 24

Views: 65432

Answers (1)

user2915097
user2915097

Reputation: 32176

group your RUN, do the wget and the tar in one RUN, something like

RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.6.0+-x64-linux.tar.gz \ && tar zxvpf ncbi-blast-2.6.0+-x64-linux.tar.gz && rm ncbi-blast-2.6.0+-x64-linux.tar.gz

See the best practices for writing Dockerfile

https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/

and use ENV instead of export in your Dockerfile

https://docs.docker.com/engine/reference/builder/#env

Upvotes: 23

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