Previously working Neurodocker image failing - IsADirectoryError


#1

Hello,

I’d previously gotten a custom Neurodocker image working, which opened as a Jupyter Notebook, but since had to clear my docker images.

What is strange is that the build worked on Monday (02/19/2018), but after having to clear my docker images and rebuild again, it would no longer work on Wednesday (02/21/2018). I’ve tried to debug this, reseting Docker to factory defaults, trying a different Neurodebian build (trust-non-free, instead of stretch-non-free as I’ve been using), but these have not solved it. I’m wondering if there may have been some update this week that broke compatibility?

Anyway, I’m posting in case anyone has thoughts on how to go about debugging this build. The problem appears to stem from this command in the Dockerfile.

#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name neuro python=3.6 \
                                jupyter \
                                jupyterlab \
                                jupyter_contrib_nbextensions \
                                traits \
                                pandas \
                                matplotlib \
                                scikit-learn \
                                seaborn \
&& sync && conda clean -tipsy && sync \
&& /bin/bash -c "source activate neuro \
  && pip install -q --no-cache-dir https://github.com/nipy/nipype/tarball/master \
                                   https://github.com/INCF/pybids/tarball/master \
                                   nilearn \
                                   datalad[full] \
                                   nipy \
                                   duecredit" \
&& sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT

Here is the neurodocker command to build the Dockerfile:

docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-free -p apt \
--install convert3d ants fsl gcc g++ graphviz tree \
          git-annex-standalone vim emacs-nox nano less ncdu \
          tig git-annex-remote-rclone \
--freesurfer version=6.0.0 min=true \
--afni version=latest \
--add-to-entrypoint "source /etc/fsl/fsl.sh" \
--spm version=12 matlab_version=R2017a \
--user=neuro \
--miniconda \
  conda_install="python=3.6 jupyter jupyterlab jupyter_contrib_nbextensions
                 traits pandas matplotlib scikit-learn seaborn" \
  pip_install="https://github.com/nipy/nipype/tarball/master
               https://github.com/INCF/pybids/tarball/master
               nilearn datalad[full] nipy duecredit" \
  env_name="neuro" \
  activate=True \
--run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
--user=root \
--miniconda \
  pip_install="git+https://github.com/poldracklab/fmriprep.git
               git+https://github.com/poldracklab/niworkflows.git" \
  env_name="neuro" \
  activate=True \
--run 'chown -R neuro /home/neuro' \
--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
--run 'mkdir /output && chmod 777 /output && chmod a+s /output' \
--user=neuro \
--workdir /home/neuro \
--cmd "jupyter-notebook" \
--no-check-urls > Dockerfile

And here is the full output of the build attempt from the resulting Dockerfile (with successful steps cached):

$ docker build --rm -t my_nipype .
Sending build context to Docker daemon  44.03kB
Step 1/30 : FROM neurodebian:stretch-non-free
 ---> 0f99b7ca24a5
Step 2/30 : ARG DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 2215f5ffcff6
Step 3/30 : ENV LANG="en_US.UTF-8"     LC_ALL="C.UTF-8"     ND_ENTRYPOINT="/neurodocker/startup.sh"
 ---> Using cache
 ---> ae4bcceb79be
Step 4/30 : RUN apt-get update -qq && apt-get install -yq --no-install-recommends      	apt-utils bzip2 ca-certificates curl locales unzip     && apt-get clean     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*     && localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8     && chmod 777 /opt && chmod a+s /opt     && mkdir -p /neurodocker     && if [ ! -f "$ND_ENTRYPOINT" ]; then          echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT          && echo 'set +x' >> $ND_ENTRYPOINT          && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT;        fi     && chmod -R 777 /neurodocker && chmod a+s /neurodocker
 ---> Using cache
 ---> ff3a7d1c0d71
Step 5/30 : ENTRYPOINT ["/neurodocker/startup.sh"]
 ---> Using cache
 ---> cf803b825a9c
Step 6/30 : RUN apt-get update -qq     && apt-get install -y -q --no-install-recommends convert3d                                                      ants                                                      fsl                                                      gcc                                                      g++                                                      graphviz                                                      tree                                                      git-annex-standalone                                                      vim                                                      emacs-nox                                                      nano                                                      less                                                      ncdu                                                      tig                                                      git-annex-remote-rclone     && apt-get clean     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ---> Using cache
 ---> d68b72540668
Step 7/30 : RUN apt-get update -qq && apt-get install -yq --no-install-recommends bc libgomp1 libxmu6 libxt6 tcsh perl     && apt-get clean     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*     && echo "Downloading minimized FreeSurfer ..."     && curl -sSL --retry 5 https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz | tar xz -C /opt     && sed -i '$isource $FREESURFER_HOME/SetUpFreeSurfer.sh' $ND_ENTRYPOINT
 ---> Using cache
 ---> 1bdb11f8da18
Step 8/30 : ENV FREESURFER_HOME=/opt/freesurfer
 ---> Using cache
 ---> 653ecdafbcc3
Step 9/30 : ENV PATH=/opt/afni:$PATH
 ---> Using cache
 ---> 1026cf261191
Step 10/30 : RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa     libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb     && libs_path=/usr/lib/x86_64-linux-gnu     && if [ -f $libs_path/libgsl.so.19 ]; then            ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0;        fi     && echo "Install libxp (not in all ubuntu/debian repositories)"     && apt-get install -yq --no-install-recommends libxp6     || /bin/bash -c "        curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb        && dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb"     && echo "Install libpng12 (not in all ubuntu/debian repositories"     && apt-get install -yq --no-install-recommends libpng12-0     || /bin/bash -c "        curl --retry 5 -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb        && dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb"     && apt-get clean     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*     && echo "Downloading AFNI ..."     && mkdir -p /opt/afni     && curl -sSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar zx -C /opt/afni --strip-components=1
 ---> Using cache
 ---> 8bdfdcec3d95
Step 11/30 : RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 ---> Using cache
 ---> c0713ba561e0
Step 12/30 : RUN apt-get update -qq && apt-get install -yq --no-install-recommends libxext6 libxt6     && apt-get clean     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*     && echo "Downloading MATLAB Compiler Runtime ..."     && curl -sSL --retry 5 -o /tmp/mcr.zip https://www.mathworks.com/supportfiles/downloads/R2017a/deployment_files/R2017a/installers/glnxa64/MCR_R2017a_glnxa64_installer.zip     && unzip -q /tmp/mcr.zip -d /tmp/mcrtmp     && /tmp/mcrtmp/install -destinationFolder /opt/mcr -mode silent -agreeToLicense yes     && rm -rf /tmp/*
 ---> Using cache
 ---> 63363c20146d
Step 13/30 : RUN echo "Downloading standalone SPM ..."     && curl -sSL --retry 5 -o spm.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2017a.zip     && unzip -q spm.zip -d /opt     && chmod -R 777 /opt/spm*     && rm -rf spm.zip     && /opt/spm12/run_spm12.sh /opt/mcr/v92/ quit     && sed -i '$iexport SPMMCRCMD=\"/opt/spm12/run_spm12.sh /opt/mcr/v92/ script\"' $ND_ENTRYPOINT
 ---> Using cache
 ---> b3b0729bff45
Step 14/30 : ENV MATLABCMD=/opt/mcr/v92/toolbox/matlab     FORCE_SPMMCR=1     LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64:$LD_LIBRARY_PATH
 ---> Using cache
 ---> 8e29826f7fba
Step 15/30 : RUN useradd --no-user-group --create-home --shell /bin/bash neuro
 ---> Using cache
 ---> 679cc11094f9
Step 16/30 : USER neuro
 ---> Using cache
 ---> 700551d8361b
Step 17/30 : ENV CONDA_DIR=/opt/conda     PATH=/opt/conda/bin:$PATH
 ---> Using cache
 ---> 46b98eabad4c
Step 18/30 : RUN echo "Downloading Miniconda installer ..."     && miniconda_installer=/tmp/miniconda.sh     && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh     && /bin/bash $miniconda_installer -b -p $CONDA_DIR     && rm -f $miniconda_installer     && conda config --system --prepend channels conda-forge     && conda config --system --set auto_update_conda false     && conda config --system --set show_channel_urls true     && conda clean -tipsy && sync
 ---> Using cache
 ---> 151b9294db01
Step 19/30 : RUN conda create -y -q --name neuro python=3.6                                     jupyter                                     jupyterlab                                     jupyter_contrib_nbextensions                                     traits                                     pandas                                     matplotlib                                     scikit-learn                                     seaborn     && sync && conda clean -tipsy && sync     && /bin/bash -c "source activate neuro       && pip install -q --no-cache-dir https://github.com/nipy/nipype/tarball/master                                        https://github.com/INCF/pybids/tarball/master                                        nilearn                                        datalad[full]                                        nipy                                        duecredit"     && sync     && sed -i '$isource activate neuro' $ND_ENTRYPOINT
 ---> Running in 9da038ddc954
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/envs/neuro

  added / updated specs: 
    - jupyter
    - jupyter_contrib_nbextensions
    - jupyterlab
    - matplotlib
    - pandas
    - python=3.6
    - scikit-learn
    - seaborn
    - traits


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    readline-7.0               |                0         838 KB  conda-forge
    testpath-0.3.1             |           py36_0          90 KB  conda-forge
    seaborn-0.8.1              |           py36_0         334 KB  conda-forge
    pcre-8.39                  |                0         725 KB  conda-forge
    jupyter_contrib_core-0.3.3 |           py36_1          28 KB  conda-forge
    scikit-learn-0.19.1        |py36_blas_openblas_201        12.8 MB  conda-forge
    ipykernel-4.8.2            |           py36_0         148 KB  conda-forge
    pyzmq-17.0.0               |           py36_3         1.1 MB  conda-forge
    numpy-1.14.1               |py36_blas_openblas_200         9.0 MB  conda-forge
    jupyter_client-5.2.2       |           py36_0         126 KB  conda-forge
    pyparsing-2.2.0            |           py36_0          95 KB  conda-forge
    pygments-2.2.0             |           py36_0         1.3 MB  conda-forge
    qtconsole-4.3.1            |           py36_0         149 KB  conda-forge
    zeromq-4.2.3               |                2         881 KB  conda-forge
    simplegeneric-0.8.1        |           py36_0           8 KB  conda-forge
    libsodium-1.0.15           |                1         1.5 MB  conda-forge
    python-dateutil-2.6.1      |           py36_0         237 KB  conda-forge
    setuptools-38.5.1          |           py36_0         524 KB  conda-forge
    freetype-2.8.1             |                0         2.9 MB  conda-forge
    icu-58.2                   |                0        22.7 MB  conda-forge
    scipy-1.0.0                |py36_blas_openblas_201        40.3 MB  conda-forge
    libpng-1.6.34              |                0         305 KB  conda-forge
    gst-plugins-base-1.8.0     |                0         4.0 MB  conda-forge
    jupyter_core-4.4.0         |             py_0          44 KB  conda-forge
    jupyter_console-5.2.0      |           py36_0          34 KB  conda-forge
    mistune-0.8.3              |             py_0          16 KB  conda-forge
    jupyter_highlight_selected_word-0.1.0|           py36_0          13 KB  conda-forge
    entrypoints-0.2.3          |           py36_1           9 KB  conda-forge
    jupyter-1.0.0              |           py36_0           3 KB  conda-forge
    pexpect-4.4.0              |           py36_0          74 KB  conda-forge
    blas-1.1                   |         openblas           1 KB  conda-forge
    ncurses-5.9                |               10         1.1 MB  conda-forge
    lxml-4.1.1                 |           py36_0         5.4 MB  conda-forge
    wcwidth-0.1.7              |           py36_0          23 KB  conda-forge
    jupyterlab-0.31.8          |           py36_1         8.5 MB  conda-forge
    backports.functools_lru_cache-1.5|           py36_0          11 KB  conda-forge
    gmp-6.1.2                  |                0         670 KB  conda-forge
    sqlite-3.20.1              |                2         1.3 MB  conda-forge
    webencodings-0.5           |           py36_0          18 KB  conda-forge
    yaml-0.1.6                 |                0         300 KB  conda-forge
    jsonschema-2.6.0           |           py36_1          64 KB  conda-forge
    jupyter_latex_envs-1.4.0   |           py36_1         738 KB  conda-forge
    xorg-libxau-1.0.8          |                3          14 KB  conda-forge
    gettext-0.19.8.1           |                0         6.3 MB  conda-forge
    jinja2-2.10                |           py36_0         183 KB  conda-forge
    prompt_toolkit-1.0.15      |           py36_0         339 KB  conda-forge
    ipython_genutils-0.2.0     |           py36_0          36 KB  conda-forge
    notebook-5.4.0             |           py36_0         6.6 MB  conda-forge
    ipywidgets-7.1.2           |           py36_0          99 KB  conda-forge
    tk-8.6.7                   |                0         3.1 MB  conda-forge
    openssl-1.0.2n             |                0         3.5 MB  conda-forge
    xorg-libxdmcp-1.1.2        |                3          21 KB  conda-forge
    sip-4.18                   |           py36_1         263 KB  conda-forge
    libxslt-1.1.32             |                0         1.4 MB  conda-forge
    pyyaml-3.12                |           py36_1         394 KB  conda-forge
    libiconv-1.15              |                0         2.0 MB  conda-forge
    backports-1.0              |           py36_1           4 KB  conda-forge
    statsmodels-0.8.0          |           py36_0         7.9 MB  conda-forge
    html5lib-1.0.1             |             py_0          89 KB  conda-forge
    zlib-1.2.11                |                0          93 KB  conda-forge
    ipython-6.2.1              |           py36_1         1.0 MB  conda-forge
    pandas-0.22.0              |           py36_0        26.1 MB  conda-forge
    jpeg-9b                    |                2         1.0 MB  conda-forge
    fontconfig-2.12.6          |                0         943 KB  conda-forge
    jupyter_nbextensions_configurator-0.4.0|           py36_0         470 KB  conda-forge
    cycler-0.10.0              |           py36_0          14 KB  conda-forge
    nbformat-4.4.0             |           py36_0         140 KB  conda-forge
    markupsafe-1.0             |           py36_0          32 KB  conda-forge
    openblas-0.2.20            |                7        17.0 MB  conda-forge
    libffi-3.2.1               |                3          47 KB  conda-forge
    patsy-0.5.0                |           py36_0         322 KB  conda-forge
    dbus-1.10.22               |                0         1.6 MB  conda-forge
    pandocfilters-1.4.1        |           py36_0          13 KB  conda-forge
    tornado-4.5.3              |           py36_0         628 KB  conda-forge
    traitlets-4.3.2            |           py36_0         131 KB  conda-forge
    traits-4.6.0               |           py36_1         468 KB  conda-forge
    bleach-2.0.0               |             py_1          20 KB  conda-forge
    xz-5.2.3                   |                0         854 KB  conda-forge
    libxml2-2.9.7              |                0         5.0 MB  conda-forge
    libgfortran-3.0.0          |                1         281 KB  defaults
    python-3.6.4               |                0        19.1 MB  conda-forge
    jupyterlab_launcher-0.10.5 |           py36_0          24 KB  conda-forge
    expat-2.2.5                |                0         434 KB  conda-forge
    jedi-0.11.1                |           py36_0         306 KB  conda-forge
    ca-certificates-2018.1.18  |                0         140 KB  conda-forge
    pickleshare-0.7.4          |           py36_0          11 KB  conda-forge
    send2trash-1.5.0           |             py_0          12 KB  conda-forge
    pytz-2018.3                |             py_0         217 KB  conda-forge
    matplotlib-2.1.2           |           py36_0         9.4 MB  conda-forge
    terminado-0.8.1            |           py36_0          20 KB  conda-forge
    ptyprocess-0.5.2           |           py36_0          22 KB  conda-forge
    six-1.11.0                 |           py36_1          21 KB  conda-forge
    gstreamer-1.8.0            |                1         3.3 MB  conda-forge
    glib-2.55.0                |                0         8.3 MB  conda-forge
    widgetsnbextension-3.1.4   |           py36_0         1.7 MB  conda-forge
    pyqt-5.6.0                 |           py36_4         5.3 MB  conda-forge
    nbconvert-5.3.1            |             py_1         320 KB  conda-forge
    qt-5.6.2                   |                7        44.3 MB  conda-forge
    wheel-0.30.0               |           py36_2          66 KB  conda-forge
    pip-9.0.1                  |           py36_1         1.7 MB  conda-forge
    pandoc-2.1.1               |                0        20.8 MB  conda-forge
    certifi-2018.1.18          |           py36_0         143 KB  conda-forge
    jupyter_contrib_nbextensions-0.4.0|           py36_0        19.4 MB  conda-forge
    parso-0.1.1                |             py_0          60 KB  conda-forge
    decorator-4.1.2            |           py36_0          15 KB  conda-forge
    libxcb-1.12                |                1         454 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       342.4 MB

The following NEW packages will be INSTALLED:

    backports:                         1.0-py36_1                    conda-forge
    backports.functools_lru_cache:     1.5-py36_0                    conda-forge
    blas:                              1.1-openblas                  conda-forge
    bleach:                            2.0.0-py_1                    conda-forge
    ca-certificates:                   2018.1.18-0                   conda-forge
    certifi:                           2018.1.18-py36_0              conda-forge
    cycler:                            0.10.0-py36_0                 conda-forge
    dbus:                              1.10.22-0                     conda-forge
    decorator:                         4.1.2-py36_0                  conda-forge
    entrypoints:                       0.2.3-py36_1                  conda-forge
    expat:                             2.2.5-0                       conda-forge
    fontconfig:                        2.12.6-0                      conda-forge
    freetype:                          2.8.1-0                       conda-forge
    gettext:                           0.19.8.1-0                    conda-forge
    glib:                              2.55.0-0                      conda-forge
    gmp:                               6.1.2-0                       conda-forge
    gst-plugins-base:                  1.8.0-0                       conda-forge
    gstreamer:                         1.8.0-1                       conda-forge
    html5lib:                          1.0.1-py_0                    conda-forge
    icu:                               58.2-0                        conda-forge
    ipykernel:                         4.8.2-py36_0                  conda-forge
    ipython:                           6.2.1-py36_1                  conda-forge
    ipython_genutils:                  0.2.0-py36_0                  conda-forge
    ipywidgets:                        7.1.2-py36_0                  conda-forge
    jedi:                              0.11.1-py36_0                 conda-forge
    jinja2:                            2.10-py36_0                   conda-forge
    jpeg:                              9b-2                          conda-forge
    jsonschema:                        2.6.0-py36_1                  conda-forge
    jupyter:                           1.0.0-py36_0                  conda-forge
    jupyter_client:                    5.2.2-py36_0                  conda-forge
    jupyter_console:                   5.2.0-py36_0                  conda-forge
    jupyter_contrib_core:              0.3.3-py36_1                  conda-forge
    jupyter_contrib_nbextensions:      0.4.0-py36_0                  conda-forge
    jupyter_core:                      4.4.0-py_0                    conda-forge
    jupyter_highlight_selected_word:   0.1.0-py36_0                  conda-forge
    jupyter_latex_envs:                1.4.0-py36_1                  conda-forge
    jupyter_nbextensions_configurator: 0.4.0-py36_0                  conda-forge
    jupyterlab:                        0.31.8-py36_1                 conda-forge
    jupyterlab_launcher:               0.10.5-py36_0                 conda-forge
    libffi:                            3.2.1-3                       conda-forge
    libgfortran:                       3.0.0-1                       defaults   
    libiconv:                          1.15-0                        conda-forge
    libpng:                            1.6.34-0                      conda-forge
    libsodium:                         1.0.15-1                      conda-forge
    libxcb:                            1.12-1                        conda-forge
    libxml2:                           2.9.7-0                       conda-forge
    libxslt:                           1.1.32-0                      conda-forge
    lxml:                              4.1.1-py36_0                  conda-forge
    markupsafe:                        1.0-py36_0                    conda-forge
    matplotlib:                        2.1.2-py36_0                  conda-forge
    mistune:                           0.8.3-py_0                    conda-forge
    nbconvert:                         5.3.1-py_1                    conda-forge
    nbformat:                          4.4.0-py36_0                  conda-forge
    ncurses:                           5.9-10                        conda-forge
    notebook:                          5.4.0-py36_0                  conda-forge
    numpy:                             1.14.1-py36_blas_openblas_200 conda-forge [blas_openblas]
    openblas:                          0.2.20-7                      conda-forge
    openssl:                           1.0.2n-0                      conda-forge
    pandas:                            0.22.0-py36_0                 conda-forge
    pandoc:                            2.1.1-0                       conda-forge
    pandocfilters:                     1.4.1-py36_0                  conda-forge
    parso:                             0.1.1-py_0                    conda-forge
    patsy:                             0.5.0-py36_0                  conda-forge
    pcre:                              8.39-0                        conda-forge
    pexpect:                           4.4.0-py36_0                  conda-forge
    pickleshare:                       0.7.4-py36_0                  conda-forge
    pip:                               9.0.1-py36_1                  conda-forge
    prompt_toolkit:                    1.0.15-py36_0                 conda-forge
    ptyprocess:                        0.5.2-py36_0                  conda-forge
    pygments:                          2.2.0-py36_0                  conda-forge
    pyparsing:                         2.2.0-py36_0                  conda-forge
    pyqt:                              5.6.0-py36_4                  conda-forge
    python:                            3.6.4-0                       conda-forge
    python-dateutil:                   2.6.1-py36_0                  conda-forge
    pytz:                              2018.3-py_0                   conda-forge
    pyyaml:                            3.12-py36_1                   conda-forge
    pyzmq:                             17.0.0-py36_3                 conda-forge
    qt:                                5.6.2-7                       conda-forge
    qtconsole:                         4.3.1-py36_0                  conda-forge
    readline:                          7.0-0                         conda-forge
    scikit-learn:                      0.19.1-py36_blas_openblas_201 conda-forge [blas_openblas]
    scipy:                             1.0.0-py36_blas_openblas_201  conda-forge [blas_openblas]
    seaborn:                           0.8.1-py36_0                  conda-forge
    send2trash:                        1.5.0-py_0                    conda-forge
    setuptools:                        38.5.1-py36_0                 conda-forge
    simplegeneric:                     0.8.1-py36_0                  conda-forge
    sip:                               4.18-py36_1                   conda-forge
    six:                               1.11.0-py36_1                 conda-forge
    sqlite:                            3.20.1-2                      conda-forge
    statsmodels:                       0.8.0-py36_0                  conda-forge
    terminado:                         0.8.1-py36_0                  conda-forge
    testpath:                          0.3.1-py36_0                  conda-forge
    tk:                                8.6.7-0                       conda-forge
IsADirectoryError(21, 'Is a directory')



    tornado:                           4.5.3-py36_0                  conda-forge
    traitlets:                         4.3.2-py36_0                  conda-forge
    traits:                            4.6.0-py36_1                  conda-forge
    wcwidth:                           0.1.7-py36_0                  conda-forge
    webencodings:                      0.5-py36_0                    conda-forge
    wheel:                             0.30.0-py36_2                 conda-forge
    widgetsnbextension:                3.1.4-py36_0                  conda-forge
    xorg-libxau:                       1.0.8-3                       conda-forge
    xorg-libxdmcp:                     1.1.2-3                       conda-forge
    xz:                                5.2.3-0                       conda-forge
    yaml:                              0.1.6-0                       conda-forge
    zeromq:                            4.2.3-2                       conda-forge
    zlib:                              1.2.11-0                      conda-forge

The command '/bin/sh -c conda create -y -q --name neuro python=3.6                                     jupyter                                     jupyterlab                                     jupyter_contrib_nbextensions                                     traits                                     pandas                                     matplotlib                                     scikit-learn                                     seaborn     && sync && conda clean -tipsy && sync     && /bin/bash -c "source activate neuro       && pip install -q --no-cache-dir https://github.com/nipy/nipype/tarball/master                                        https://github.com/INCF/pybids/tarball/master                                        nilearn                                        datalad[full]                                        nipy                                        duecredit"     && sync     && sed -i '$isource activate neuro' $ND_ENTRYPOINT' returned a non-zero code: 1

#2

This is related to a bug in conda - see https://github.com/poldracklab/niworkflows/pull/227


#3

Hi @jordan_theriault, to fix the error that @ChrisGorgolewski mentioned, you can include the argument miniconda_version="4.3.31" in the --miniconda section of your command. By default, the latest Miniconda is installed (which is currently 4.4.10, the bugged version).


#4

This worked! Thank you!

Although the command should not have the version in quotation, so the line to add is: miniconda_version=4.3.31 for anyone who finds this in the future (by which point this bug should be a non-issue anyway).