pnlbwh / fsl-containers Goto Github PK

Howdy,

This is a continuation of this issue: Path to conda not specified. Posting here in hopes that it might help someone else later on.

I've changed the following code to reflect the link tot he most current release of fsl (6.0.7.4)

# install FSL, -V 6.0.7.4, you are welcome to change it below RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -O fslinstaller.py \ && python fslinstaller.py -V 6.0.7.4 -d $PWD/fsl-6.0.7.4-centos7

I've also changed the final RUN command to

RUN $FSLDIR/condabin/conda install -y -n fslpython -c conda-forge deprecation

When building the image I now get this error:

ERROR [5/5] RUN /root/fsl-6.0.7.4-centos7/condabin/conda install -y -n fslpython -c conda-forge deprecation 0.6s

[5/5] RUN /root/fsl-6.0.7.4-centos7/condabin/conda install -y -n fslpython -c conda-forge deprecation:
0.514 EnvironmentLocationNotFound: Not a conda environment: /root/fsl-6.0.7.4-centos7/envs/fslpython
0.514

Dockerfile.centos7:34

32 | # RUN $FSLDIR/fslpython/bin/conda install -y -n fslpython -c conda-forge deprecation==1.*
33 | # RUN $FSLDIR/condabin/conda install -y -n fslpython -c conda-forge deprecation==1.*
34 | >>> RUN $FSLDIR/condabin/conda install -y -n fslpython -c conda-forge deprecation

ERROR: failed to solve: process "/bin/sh -c $FSLDIR/condabin/conda install -y -n fslpython -c conda-forge deprecation" did not complete successfully: exit code: 1

I found the file path for the final RUN command by creating the docker image without the final line (since that was the one giving the error), running the image in a container, and looking through the file directory. The docker image builds properly, and the container runs properly, but the gui does not appear in the windows x server (VcXserv).

The following is from that process:

[root@245282c3752b ~]# ls
anaconda-ks.cfg fsl-6.0.7.4-centos7 fslinstaller.py

[root@245282c3752b ~]# ls fsl-6.0.7.4
ls: cannot access fsl-6.0.7.4: No such file or directory

[root@245282c3752b ~]# ls fsl-6.0.7.4-centos7
LICENCE.FSL bin compiler_compat condabin data envs fonts lib man phrasebooks plugins qml share src tcl var x86_64-conda_cos6-linux-gnu LICENSE.txt cmake conda-meta config doc etc include libexec mkspecs pkgs python sbin shell ssl translations x86_64-conda-linux-gnu

[root@245282c3752b ~]# ls fsl-6.0.7.4-centos7/condabin
conda mamba

[root@245282c3752b ~]# ls fsl-6.0.7.4-centos7/envs (envs is empty)

[root@245282c3752b ~]# Feat (This fails to find the display)

Your help is greatly appreciated!