update docker image (#410)

* badge update

* badge test

* func output tree overhaul

* concurant func and dwi pipelines

* sort functional and diffusion output folder organization

* m2g-f file output fix

* remove iteration output

* update for travis test

* readme update

* readme update

* remove travis

* update file output

* pass push check

* Docker file overhaul, switch base image to neurodebian: bionic-non-free

* initial stable dockerfile

* first round of version control for dockerfile

* change cpac runner to python3.7

* fix missing module issue by making them visible to python3, also change installation order

* vix missing xvfbwrapper

* instruction update

* update

* README update

* finish file definition

* README rough draft

* remove lfs requirement

Dockerfile

@@ -32,20 +32,12 @@ RUN apt-get update && \
 RUN pip3.7 install --upgrade pip
 
 
-# Get neurodebian config
-# RUN curl -sSL http://neuro.debian.net/lists/stretch.us-tn.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-#     apt-key add /root/.neurodebian.gpg && \
-#     (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) && \
-#     apt-get update -qq
-# RUN apt-get -f install
-
-
 
 # Configure git-lfs
-RUN apt-get install -y apt-transport-https debian-archive-keyring
-RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
-    apt-get update && \
-    apt-get install -y git-lfs
+# RUN apt-get install -y apt-transport-https debian-archive-keyring
+# RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
+#     apt-get update && \
+#     apt-get install -y git-lfs
 
 # #---------AFNI INSTALL--------------------------------------------------------#
 # # setup of AFNI, which provides robust modifications of many of neuroimaging algorithms
@@ -197,27 +189,22 @@ RUN apt-get update && apt-get -y upgrade insighttoolkit4-python
 # setup of python dependencies for m2g itself, as well as file dependencies
 RUN \
     pip3.7 install --no-cache-dir hyppo==0.1.3 nibabel==2.3.3 scipy==1.4.1 python-dateutil pandas==0.23.4 boto3==1.7.13 awscli==1.15.40 virtualenv
+
 RUN \
     pip3.7 install --no-cache-dir matplotlib nilearn sklearn cython vtk pyvtk fury==0.5.1
 RUN \
     pip3.7 install --no-cache-dir yamlordereddictloader
-#got rid of awscli here^
 RUN \
+
     pip3.7 install --no-cache-dir requests ipython duecredit graspy==0.3.0 scikit-image networkx dipy==1.1.1 pybids==0.12.0
 
 # TODO: Update pybids
 RUN \
     pip3.7 install --no-cache-dir plotly==1.12.9 configparser>=3.7.4 regex
 
-
-RUN \
-    pip3.7 install s3transfer==0.3.7
-
-RUN \
-    pip3.7 install setuptools==57.5.0
 
 RUN \
-    pip3.7 install numba==0.52.0
+    pip3.7 install s3transfer==0.3.7 setuptools==57.5.0 numba==0.52.0
 
 # install ICA-AROMA
 RUN mkdir -p /opt/ICA-AROMA
@@ -276,7 +263,7 @@ RUN pip3.7 install git+https://github.com/ChildMindInstitute/PyPEER.git
 RUN mkdir /m2g_atlases
 
 RUN \
-    git clone https://github.com/neurodata/neuroparc -b remove-lfs && \
+    git clone https://github.com/neurodata/neuroparc && \
     mv /neuroparc/atlases /m2g_atlases && \
     rm -rf /neuroparc
 RUN chmod -R 777 /m2g_atlases