fsl 6.0.3 install failing

[poldrack]

Using the following command on Mac OS 10.15.7 with Docker version 20.10.6:

docker run --rm repronim/neurodocker:0.7.0 generate docker \
    --base debian:stretch --pkg-manager apt --fsl version=6.0.3

I get the following error:

#7 15.46 Downloading FSL ...
#7 654.4 Installing FSL conda environment ...
#7 664.4 Stage 1
#7 664.4 By installing this python distribution you agree to the license terms in
#7 664.4 /opt/fsl-6.0.3/fslpython/LICENSE.txt
100%64.4
#7 674.1 Stage 2
100%74.4
#7 743.2 /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh: line 206:  1439 Killed                  FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create -f "${script_dir}/fslpython_environment.yml" 2>> "${miniconda_install_log}"
#7 743.2       1440 Done                    | ${script_dir}/progress.sh 133 ${quiet} >> "${miniconda_install_log}"
#7 743.2 Failed to create FSL Python environment - see /tmp/fslpythonTwKA/fslpython_miniconda_installer.log for details
------
executor failed running [/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            bc            dc            file            libfontconfig1            libfreetype6            libgl1-mesa-dev            libgl1-mesa-dri            libglu1-mesa-dev            libgomp1            libice6            libxcursor1            libxft2            libxinerama1            libxrandr2            libxrender1            libxt6            sudo            wget     && apt-get clean     && rm -rf /var/lib/apt/lists/*     && echo "Downloading FSL ..."     && mkdir -p /opt/fsl-6.0.3     && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz     | tar -xz -C /opt/fsl-6.0.3 --strip-components 1     && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT     && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT     && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT     && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT     && echo "Installing FSL conda environment ..."     && bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3]: exit code: 4
make: *** [build] Error 1

[PatrikBey]

Hi,

has there been a solution to this issue? I'm still running into it when installing fsl 6.0.4 during a docker build call.

`------

[ 9/11] RUN /usr/local/fsl/etc/fslconf/fslpython_install.sh -f /usr/local/fsl: #12 5.856 Stage 1 #12 5.856 By installing this python distribution you agree to the license terms in #12 5.856 /usr/local/fsl/fslpython/LICENSE.txt 100%5.870 #12 18.23 Stage 2 100%59.97 #12 538.4 #12 538.4 ----- ERROR ----- #12 538.4 #12 538.4 Failed to create FSL Python environment - see /tmp/fslpythonUHgE/fslpython_miniconda_installer.log for details ------ executor failed running [/bin/sh -c /usr/local/fsl/etc/fslconf/fslpython_install.sh -f /usr/local/fsl]: exit code: 4 `

[award7]

I can't even get v6.0.3 to finish building.

[kaczmarj]

@djarecka @satra - could someone please help with debugging this issue?

[PatrikBey]

Hey

I found the following installation instruction to work for FSL 6.0.4 inside the DOCKERFILE for my container:

RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
    chmod 775 fslinstaller.py && \
    python2 /fslinstaller.py -d /opt/fsl -V 6.0.4 -q && \
    rm -f /fslinstaller.py

RUN rm -rf /opt/fsl/fslpython && \
   /opt/fsl/etc/fslconf/fslpython_install.sh -f /opt/fsl 

It only seemed to work for a Ubuntu:18.04 though not my previous 20:04. Hope this helps.

[EvelinYin]

Hey

I found the following installation instruction to work for FSL 6.0.4 inside the DOCKERFILE for my container:

RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
    chmod 775 fslinstaller.py && \
    python2 /fslinstaller.py -d /opt/fsl -V 6.0.4 -q && \
    rm -f /fslinstaller.py

RUN rm -rf /opt/fsl/fslpython && \
   /opt/fsl/etc/fslconf/fslpython_install.sh -f /opt/fsl 

It only seemed to work for a Ubuntu:18.04 though not my previous 20:04. Hope this helps.

I get the following error: failed to solve with frontend dockerfile.v0: failed to create LLB definition: no build stage in current context

[kaczmarj]

Hey I found the following installation instruction to work for FSL 6.0.4 inside the DOCKERFILE for my container:

RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
    chmod 775 fslinstaller.py && \
    python2 /fslinstaller.py -d /opt/fsl -V 6.0.4 -q && \
    rm -f /fslinstaller.py

RUN rm -rf /opt/fsl/fslpython && \
   /opt/fsl/etc/fslconf/fslpython_install.sh -f /opt/fsl 

It only seemed to work for a Ubuntu:18.04 though not my previous 20:04. Hope this helps.

I get the following error: failed to solve with frontend dockerfile.v0: failed to create LLB definition: no build stage in current context

Try adding a FROM ubuntu:18.04 at the top.

[JohannesWiesner]

Similar error here (script has been stuck at "stage 2" for more than 12hrs now):

This seems to be documented on neurostars

[JohannesWiesner]

This code section (derived from this comment on neurostars) worked for me.

[Remi-Gau]

For the record this is the case for all base image that we test on:

https://github.com/ReproNim/neurodocker/blob/test_docker_build/docs/README.md#fsl

[github-actions[bot]]

This issue is stale because it has been open for 30 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.

[Remi-Gau]

given that the dashboard covers this use case, I am OK with keeping this one closed

we basically have install issues with FSL 6.0.2 to 6.0.5

https://camo.githubusercontent.com/09089e5e5ec4b4f7f29e8105da70781fc049f710010ab835b9291b3761e05356/687474703a2f2f6769746875622d616374696f6e732e3430616e74732e636f6d2f526570726f4e696d2f6e6575726f646f636b65722f6d61747269782e7376673f6272616e63683d746573745f646f636b65725f6275696c64266f6e6c793d66736c