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bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer
Apache License 2.0
41 stars 35 forks source link

Build with local freesurfer #47

Closed Youguang closed 5 years ago

Youguang commented 5 years ago

I want to build the docker image manually with previous downloaded freesurfer to save time.

I copied freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz and license.txt into the BIDS-Apps/freesurfer clone folder, then modified the Dockerfile head part:

FROM ubuntu:16.04

RUN tar --no-same-owner -C /opt \
    --exclude='freesurfer/trctrain' \
    --exclude='freesurfer/subjects/fsaverage_sym' \
    --exclude='freesurfer/subjects/fsaverage3' \
    --exclude='freesurfer/subjects/fsaverage4' \
    --exclude='freesurfer/subjects/fsaverage5' \
    --exclude='freesurfer/subjects/fsaverage6' \
    --exclude='freesurfer/subjects/cvs_avg35' \
    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
    --exclude='freesurfer/subjects/bert' \
    --exclude='freesurfer/subjects/V1_average' \
    --exclude='freesurfer/average/mult-comp-cor' \
    --exclude='freesurfer/lib/cuda' \
    --exclude='freesurfer/lib/qt'   \
    -zxvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

COPY license.txt /opt/freesurfer/

RUN apt-get update
RUN apt-get install -y python3
...

I pulled ubuntu first: docker pull ubuntu:16.04

Then build: docker build -t fresurfer:6.0.0 .

And get this error:

Sending build context to Docker daemon  4.918GB
Step 1/48 : FROM ubuntu:16.04
 ---> 5e13f8dd4c1a
Step 2/48 : RUN tar --no-same-owner -C /opt     --exclude='freesurfer/trctrain'     --exclude='freesurfer/subjects/fsaverage_sym'     --exclude='freesurfer/subjects/fsaverage3'     --exclude='freesurfer/subjects/fsaverage4'     --exclude='freesurfer/subjects/fsaverage5'     --exclude='freesurfer/subjects/fsaverage6'     --exclude='freesurfer/subjects/cvs_avg35'     --exclude='freesurfer/subjects/cvs_avg35_inMNI152'     --exclude='freesurfer/subjects/bert'     --exclude='freesurfer/subjects/V1_average'     --exclude='freesurfer/average/mult-comp-cor'     --exclude='freesurfer/lib/cuda'     --exclude='freesurfer/lib/qt'       -zxvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
 ---> Running in 6428bc61f682
tar (child): freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
The command '/bin/sh -c tar --no-same-owner -C /opt     --exclude='freesurfer/trctrain'     --exclude='freesurfer/subjects/fsaverage_sym'     --exclude='freesurfer/subjects/fsaverage3'     --exclude='freesurfer/subjects/fsaverage4'     --exclude='freesurfer/subjects/fsaverage5'     --exclude='freesurfer/subjects/fsaverage6'     --exclude='freesurfer/subjects/cvs_avg35'     --exclude='freesurfer/subjects/cvs_avg35_inMNI152'     --exclude='freesurfer/subjects/bert'     --exclude='freesurfer/subjects/V1_average'     --exclude='freesurfer/average/mult-comp-cor'     --exclude='freesurfer/lib/cuda'     --exclude='freesurfer/lib/qt'       -zxvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz' returned a non-zero code: 2