No module named 'conda' error on docker build

[HaukeBartsch]

I am trying to docker build: docker build -t bids/hcppipelines -f Dockerfile . on MacOS and I get the following error:

... The following packages will be UPDATED:

ca-certificates: 2018.03.07-0                              --> 2019.9.11-hecc5488_0 conda-forge
certifi:         2018.4.16-py27_0                          --> 2019.9.11-py37_0     conda-forge
libffi:          3.2.1-hd88cf55_4                          --> 3.2.1-he1b5a44_1006  conda-forge
libgcc-ng:       7.2.0-hdf63c60_3                          --> 9.1.0-hdf63c60_0                
libstdcxx-ng:    7.2.0-hdf63c60_3                          --> 9.1.0-hdf63c60_0                
ncurses:         6.1-hf484d3e_0                            --> 6.1-hf484d3e_1002    conda-forge
openssl:         1.0.2o-h20670df_0                         --> 1.1.1c-h516909a_0    conda-forge
pip:             10.0.1-py27_0                             --> 19.2.3-py37_0        conda-forge
python:          2.7.15-h1571d57_0                         --> 3.7.3-h33d41f4_1     conda-forge
readline:        7.0-ha6073c6_4                            --> 8.0-hf8c457e_0       conda-forge
setuptools:      39.2.0-py27_0                             --> 41.2.0-py37_0        conda-forge
six:             1.11.0-py27h5f960f1_1                     --> 1.12.0-py37_1000     conda-forge
sqlite:          3.23.1-he433501_0                         --> 3.29.0-hcee41ef_1    conda-forge
tk:              8.6.7-hc745277_3                          --> 8.6.9-hed695b0_1003  conda-forge
wheel:           0.31.1-py27_0                             --> 0.33.6-py37_0        conda-forge
zlib:            1.2.11-ha838bed_2                         --> 1.2.11-h516909a_1006 conda-forge

Downloading and Extracting Packages Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Traceback (most recent call last): File "/usr/local/miniconda/bin/conda", line 7, in from conda.cli import main ModuleNotFoundError: No module named 'conda' The command '/bin/sh -c curl -fsSLO https://repo.continuum.io/miniconda/Miniconda2-4.5.4-Linux-x86_64.sh && bash Miniconda2-4.5.4-Linux-x86_64.sh -b -p /usr/local/miniconda && rm Miniconda2-4.5.4-Linux-x86_64.sh && conda config --add channels conda-forge && conda install -y mkl=2019.3 mkl-service=2.0.2 numpy=1.16.4 nibabel=2.4.1 pandas=0.24.2 && sync && conda clean -tipsy && sync && pip install --no-cache-dir pybids==0.9.1' returned a non-zero code: 1

[HaukeBartsch]

FYI: the error seems to be caused by:

conda clean -tipsy Traceback (most recent call last): File "/usr/local/miniconda/bin/conda", line 7, in from conda.cli import main ModuleNotFoundError: No module named 'conda'

I can run all other commands in that section just fine.

[HaukeBartsch]

One more problem is with downloading the workbench:

wget https://ftp.humanconnectome.org/workbench/workbench-linux64-v1.3.2.zip --2019-09-24 13:45:04-- https://ftp.humanconnectome.org/workbench/workbench-linux64-v1.3.2.zip Resolving ftp.humanconnectome.org (ftp.humanconnectome.org)... 128.252.155.86 Connecting to ftp.humanconnectome.org (ftp.humanconnectome.org)|128.252.155.86|:443... connected. Unable to establish SSL connection.

I don't get anything with ftp and http either. Maybe the server is down right now?

[rhancockn]

Until the Dockerfile is updated, you could try pulling the container from rhancock/hcpbids

On Sep 24, 2019, at 7:40 AM, Hauke Bartsch notifications@github.com wrote:

 FYI: the error seems to be caused by:

conda clean -tipsy Traceback (most recent call last): File "/usr/local/miniconda/bin/conda", line 7, in from conda.cli import main ModuleNotFoundError: No module named 'conda'

I can run all other commands in that section just fine.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[rhancockn]

Closing old issues that are likely no longer applicable.