Merge pull request #41 from CoBrALab/updates

Updated the version of nilearn on the conda environment and changed the installation process to install the archive files for specific versions.

Author: Gab-D-G

Dockerfile

@@ -124,30 +124,31 @@ RUN export PATH="$HOME/miniconda-latest/bin:$PATH" \
 
 
 #### install RABIES
-
-RUN git clone https://github.com/CoBrALab/RABIES temp/RABIES && \
-  conda env create -f temp/RABIES/rabies_environment.yml && \
-  bash temp/RABIES/install.sh && \
-  rm -r temp
-
-# create WM and CSF masks
-ENV DSURQE_100micron_anat=/home/rabies/RABIES/template_files/DSURQE_100micron_average.nii.gz \
-  DSURQE_100micron_mask=/home/rabies/RABIES/template_files/DSURQE_100micron_mask.nii.gz \
-  DSURQE_100micron_labels=/home/rabies/RABIES/template_files/DSURQE_100micron_labels.nii.gz \
-  csv_labels=/home/rabies/RABIES/template_files/DSURQE_40micron_R_mapping.csv
-
-RUN /home/rabies/miniconda-latest/envs/rabies/bin/python /home/rabies/RABIES/gen_masks.py $DSURQE_100micron_labels $csv_labels /home/rabies/RABIES/template_files/DSURQE_100micron
-
-
-#write container execution script
-RUN echo "#! /home/rabies/miniconda-latest/envs/rabies/bin/python" > /home/rabies/RABIES/exec.py && \
-  echo "import os" >> /home/rabies/RABIES/exec.py && \
-  echo "import sys" >> /home/rabies/RABIES/exec.py && \
-  echo "os.environ['RABIES'] = '/home/rabies/RABIES'" >> /home/rabies/RABIES/exec.py && \
-  echo "sys.path.insert(0,os.environ['RABIES'])" >> /home/rabies/RABIES/exec.py && \
-  echo "from rabies.run_main import execute_workflow" >> /home/rabies/RABIES/exec.py && \
-  echo "execute_workflow()" >> /home/rabies/RABIES/exec.py && \
-  chmod +x /home/rabies/RABIES/exec.py
+ENV export RABIES_VERSION=0.1.1 \
+    export RABIES=$HOME/RABIES-${RABIES_VERSION} \
+    export PYTHONPATH="${PYTHONPATH}:$RABIES"
+
+RUN export RABIES_VERSION=0.1.1 && \
+  export RABIES=$HOME/RABIES-${RABIES_VERSION} && \
+  mkdir -p temp && \
+  curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \
+  cd temp && \
+  tar zxf RABIES.tar.gz && \
+  cd .. && \
+  conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \
+  bash temp/RABIES-${RABIES_VERSION}/install.sh && \
+  rm -r temp && \
+  DSURQE_100micron_labels=${RABIES}/template_files/DSURQE_100micron_labels.nii.gz && \
+  csv_labels=${RABIES}/template_files/DSURQE_40micron_R_mapping.csv && \
+  /home/rabies/miniconda-latest/envs/rabies/bin/python ${RABIES}/gen_masks.py $DSURQE_100micron_labels $csv_labels ${RABIES}/template_files/DSURQE_100micron && \
+  echo "#! /home/rabies/miniconda-latest/envs/rabies/bin/python" > ${RABIES}/exec.py && \
+  echo "import os" >> ${RABIES}/exec.py && \
+  echo "import sys" >> ${RABIES}/exec.py && \
+  echo "os.environ['RABIES'] = '${RABIES}'" >> ${RABIES}/exec.py && \
+  echo "sys.path.insert(0,os.environ['RABIES'])" >> ${RABIES}/exec.py && \
+  echo "from rabies.run_main import execute_workflow" >> ${RABIES}/exec.py && \
+  echo "execute_workflow()" >> ${RABIES}/exec.py && \
+  chmod +x ${RABIES}/exec.py
 
 ENV QBATCH_SYSTEM local
 

install.sh

@@ -1,16 +1,22 @@
 ### setup RABIES execution and DSURQE atlas
 
 #will install RABIES in HOME directory
-export RABIES=$HOME/RABIES
+export RABIES_VERSION=0.1.1
+export RABIES=$HOME/RABIES-${RABIES_VERSION}
 export PYTHONPATH="${PYTHONPATH}:$RABIES"
 
-git clone https://github.com/CoBrALab/RABIES $HOME/RABIES
+#cd $HOME
+#curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz
+#tar zxf $HOME/RABIES.tar.gz
+#rm $HOME/RABIES.tar.gz
+git clone https://github.com/CoBrALab/RABIES $RABIES
 
 #creates an executable script to execute rabies
 mkdir -p $RABIES/bin
 echo -e '#! /usr/bin/env python \nfrom rabies.run_main import execute_workflow \nexecute_workflow()' > $RABIES/bin/rabies
 chmod +x $RABIES/bin/rabies
 echo "# added by RABIES" >> $HOME/.bashrc
+echo "export RABIES_VERSION=0.1.1" >> $HOME/.bashrc
 echo "export RABIES=$RABIES" >> $HOME/.bashrc
 echo 'export PYTHONPATH="${PYTHONPATH}:$RABIES"' >> $HOME/.bashrc
 echo 'export PATH=$PATH:$RABIES/bin' >> $HOME/.bashrc

rabies_environment.yml

@@ -1,34 +1,18 @@
 name: rabies
 channels:
-  - simpleitk
   - defaults
   - conda-forge
+  - bioconda
+  - simpleitk
 dependencies:
-  - blas=2.11=openblas
-  - keepalive=0.5=py_1
-  - libblas=3.8.0=11_openblas
-  - libcblas=3.8.0=11_openblas
-  - liblapack=3.8.0=11_openblas
-  - liblapacke=3.8.0=11_openblas
-  - multiprocess=0.70.8=py36h516909a_1
-  - nibabel=2.3.1=pyh24bf2e0_0
-  - nilearn=0.4.2=pyh24bf2e0_0
-  - nipype=1.1.4=py36_0
-  - pathos=0.2.4=py_0
-  - pox=0.2.6=py_0
-  - ppft=1.6.6.1=py36_0
-  - prov=1.5.0=py36_0
-  - pydicom=1.3.0=py_0
-  - rdflib=4.2.2=py36_1000
-  - sparqlwrapper=1.8.2=py36_1000
-  - xvfbwrapper=0.2.9=py36_1000
   - _libgcc_mutex=0.1=main
   - apipkg=1.5=py36_0
   - atomicwrites=1.3.0=py36_1
   - attrs=19.1.0=py36_1
-  - ca-certificates=2019.5.15=1
+  - blas=2.11=openblas
+  - ca-certificates=2019.10.16=0
   - cairo=1.14.12=h8948797_3
-  - certifi=2019.6.16=py36_1
+  - certifi=2019.9.11=py36_0
   - click=7.0=py36_0
   - cloudpickle=1.2.2=py_0
   - cycler=0.10.0=py36_0
@@ -59,11 +43,16 @@ dependencies:
   - importlib_metadata=0.19=py36_0
   - isodate=0.6.0=py_1
   - jpeg=9b=h024ee3a_2
+  - keepalive=0.5=py_1
   - kiwisolver=1.1.0=py36he6710b0_0
+  - libblas=3.8.0=11_openblas
+  - libcblas=3.8.0=11_openblas
   - libedit=3.1.20181209=hc058e9b_0
   - libffi=3.2.1=hd88cf55_4
   - libgcc-ng=9.1.0=hdf63c60_0
   - libgfortran-ng=7.3.0=hdf63c60_0
+  - liblapack=3.8.0=11_openblas
+  - liblapacke=3.8.0=11_openblas
   - libopenblas=0.3.6=h5a2b251_1
   - libpng=1.6.37=hbc83047_0
   - libstdcxx-ng=9.1.0=hdf63c60_0
@@ -76,22 +65,31 @@ dependencies:
   - matplotlib=3.1.1=py36h5429711_0
   - mock=3.0.5=py36_0
   - more-itertools=7.2.0=py36_0
+  - multiprocess=0.70.8=py36h516909a_1
   - ncurses=6.1=he6710b0_1
   - networkx=2.3=py_0
+  - nibabel=2.3.1=pyh24bf2e0_0
+  - nilearn=0.5.2=pyh24bf2e0_0
+  - nipype=1.1.4=py36_0
   - numpy=1.16.2=py36h99e49ec_0
   - numpy-base=1.16.2=py36h2f8d375_0
   - olefile=0.46=py36_0
-  - openssl=1.1.1d=h7b6447c_1
+  - openssl=1.1.1d=h7b6447c_3
   - packaging=19.1=py36_0
   - pandas=0.25.1=py36he6710b0_0
   - pango=1.42.4=h049681c_0
+  - pathos=0.2.4=py_0
   - pcre=8.43=he6710b0_0
   - pillow=6.1.0=py36h34e0f95_0
   - pip=19.2.2=py36_0
   - pixman=0.38.0=h7b6447c_0
   - pluggy=0.12.0=py_0
+  - pox=0.2.6=py_0
+  - ppft=1.6.6.1=py36_0
+  - prov=1.5.0=py36_0
   - psutil=5.6.3=py36h7b6447c_0
   - py=1.8.0=py36_0
+  - pydicom=1.3.0=py_0
   - pydotplus=2.0.2=py36_1
   - pyparsing=2.4.2=py_0
   - pyqt=5.9.2=py36h05f1152_2
@@ -104,14 +102,17 @@ dependencies:
   - pytz=2019.2=py_0
   - pywavelets=1.0.3=py36hdd07704_1
   - qt=5.9.7=h5867ecd_1
+  - rdflib=4.2.2=py36_1000
   - readline=7.0=h7b6447c_5
   - scikit-image=0.15.0=py36he6710b0_0
   - scikit-learn=0.20.0=py36h22eb022_1
   - scipy=1.3.1=py36he2b7bc3_0
   - setuptools=41.0.1=py36_0
+  - simpleitk=1.2.2=py36hf484d3e_0
   - simplejson=3.16.0=py36h14c3975_0
   - sip=4.19.8=py36hf484d3e_0
   - six=1.12.0=py36_0
+  - sparqlwrapper=1.8.2=py36_1000
   - sqlite=3.29.0=h7b6447c_0
   - tk=8.6.8=hbc83047_0
   - toolz=0.10.0=py_0
@@ -121,17 +122,15 @@ dependencies:
   - wcwidth=0.1.7=py36_0
   - webencodings=0.5.1=py36_1
   - wheel=0.33.4=py36_0
+  - xvfbwrapper=0.2.9=py36_1000
   - xz=5.2.4=h14c3975_4
   - zipp=0.5.2=py_0
   - zlib=1.2.11=h7b6447c_3
   - zstd=1.3.7=h0b5b093_0
-  - simpleitk=1.2.2=py36hf484d3e_0
   - pip:
     - bids-validator==1.2.4
-    - dask==2.3.0
     - docopt==0.6.2
     - num2words==0.5.10
     - patsy==0.5.1
-    - pybids==0.9.4
+    - pybids==0.9.5
     - sqlalchemy==1.3.10
-