Skip to content

Completed file dialog #31

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Completed file dialog #31

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
db5d447
Completed file dialog
uhq1 Mar 19, 2019
b21b87f
recipe changes for extensions
asankar Apr 4, 2019
0f2ae42
changed Dockerfile
asankar May 7, 2019
01c0638
modified build and run
asankar May 7, 2019
79ae617
del select mult
asankar May 7, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 14 additions & 7 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
# _|_| \|||_| \| ||_|_/_|_/--\||_ _|_| |/--\\_||_
###############################################################################################

FROM murphylab/matlabmcr2018b-jupyter as intermediate
FROM murphylab/matlabmcr2018b-jupyter:18.04 as intermediate

###############################################################################################
# INSTALL BFTOOLS
Expand All @@ -24,8 +24,8 @@ RUN echo "Downloading CellOrganizer v2.8.0" && \
wget -nc --quiet http://www.cellorganizer.org/Downloads/v2.8.0/docker/cellorganizer-binaries-matlabmcr2018b.tgz && \
tar -xvf cellorganizer-binaries-matlabmcr2018b.tgz && \
rm cellorganizer-binaries-matlabmcr2018b.tgz && \
mv cellorganizer-binaries /opt

mv cellorganizer-binaries /opt
COPY tiff2ometiff /opt/cellorganizer-binaries
RUN mkdir /home/murphylab/cellorganizer-python && mkdir /home/murphylab/cellorganizer
COPY cellorganizer-python /home/murphylab/cellorganizer-python
###############################################################################################
Expand Down Expand Up @@ -55,7 +55,7 @@ COPY files /home/murphylab/cellorganizer
###############################################################################################
# COPY CELLORGANIZER LOGO TO JUPYTER NOTEBOOK
RUN wget --quiet -nc http://www.cellorganizer.org/Downloads/v2.8.0/docker/logo.png && \
mv -v logo.png /opt/conda/lib/python3.6/site-packages/notebook/static/base/images
mv -v logo.png /opt/conda/lib/python3.7/site-packages/notebook/static/base/images
###############################################################################################

###############################################################################################
Expand All @@ -65,7 +65,7 @@ RUN wget --quiet -nc http://www.cellorganizer.org/Downloads/v2.8.0/docker/logo.p
#
###############################################################################################

FROM murphylab/matlabmcr2018b-jupyter
FROM murphylab/matlabmcr2018b-jupyter:18.04

###############################################################################################
MAINTAINER Ivan E. Cao-Berg <[email protected]>
Expand All @@ -92,11 +92,13 @@ RUN chmod +x /opt/cellorganizer-binaries/img2slml && \
chmod +x /opt/cellorganizer-binaries/slml2report && \
chmod +x /opt/cellorganizer-binaries/slml2info && \
chmod +x /opt/cellorganizer-binaries/slml2slml && \
chmod +x /opt/cellorganizer-binaries/tiff2ometiff && \
ln -s /opt/cellorganizer-binaries/img2slml /usr/local/bin/img2slml && \
ln -s /opt/cellorganizer-binaries/slml2img /usr/local/bin/slml2img && \
ln -s /opt/cellorganizer-binaries/slml2report /usr/local/bin/slml2report && \
ln -s /opt/cellorganizer-binaries/slml2info /usr/local/bin/slml2info && \
ln -s /opt/cellorganizer-binaries/slml2slml /usr/local/bin/slml2slml
ln -s /opt/cellorganizer-binaries/slml2slml /usr/local/bin/slml2slml && \
ln -s /opt/cellorganizer-binaries/tiff2ometiff /usr/local/bin/tiff2ometiff

# COPY HOME DIRECTORY FROM INTERMEDIATE TO FINAL IMAGE
COPY --from=intermediate /home/murphylab /home/murphylab
Expand All @@ -107,7 +109,12 @@ RUN cd /home/murphylab/cellorganizer-python && python setup.py install
RUN rm -rf /home/murphylab/cellorganizer-python

# MOVE LOGO FROM INTERMEDIATE TO FINAL IMAGE
COPY --from=intermediate /opt/conda/lib/python3.6/site-packages/notebook/static/base/images/logo.png /opt/conda/lib/python3.6/site-packages/notebook/static/base/images/logo.png
COPY --from=intermediate /opt/conda/lib/python3.7/site-packages/notebook/static/base/images/logo.png /opt/conda/lib/python3.7/site-packages/notebook/static/base/images/logo.png

# Install Extensions
RUN conda install -c conda-forge jupyter_contrib_nbextensions
RUN jupyter nbextension enable hide_input_all/main
RUN jupyter nbextension enable init_cell/main
###############################################################################################

##############################################################################################\
Expand Down
2 changes: 1 addition & 1 deletion build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,5 @@ git submodule update
cd cellorganizer-python
git checkout master
cd ..
docker build --no-cache -t $(whoami)/cellorganizer-jupyter .
docker build -t $(whoami)/cellorganizer-jupyter .

2 changes: 1 addition & 1 deletion cellorganizer-python
Open in desktop
Submodule cellorganizer-python updated 1 files
+183 −27 cellorganizer/tools.py
20 changes: 19 additions & 1 deletion run.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,21 @@
#!/bin/bash

docker run --rm -p 8888:8888 -e JUPYTER_LAB_ENABLE=yes murphylab/cellorganizer-jupyter
if [ ! -d data ]; then
mkdir -p data/images
cd data/images
wget -nc http://murphylab.web.cmu.edu/data/TcellModels/LATFull.tgz
tar -xvf LATFull.tgz
rm -fv LATFull.tgz

wget -nc http://murphylab.web.cmu.edu/data/Hela/3D/multitiff/cellorganizer_full_image_collection.zip
unzip cellorganizer_full_image_collection.zip
rm -fv cellorganizer_full_image_collection.zip
cd ../..
fi

docker run --rm -p 8888:8888 \
-v $(pwd)/data:/home/murphylab/cellorganizer/local \
--memory="8g" \
--cpus=2 \
-e JUPYTER_LAB_ENABLE=yes \
murphylab/cellorganizer-jupyter