Setup & Running OpenVibSpec
After downloading the Dockerfile into your build folder, change your present working directory to that folder and invoke the following command. Docker will build the image without any further ado. If you encounter any problems with your build, please contact the maintainers.
docker build . -t openvibspec/anaconda3
To run openvibspec/anaconda3 with docker invoke the following command. Prerequisites, being writeable by user uid/gid 1000 (default image).
docker run -it -v <your-notebook-folder>:/opt/notebooks -p 8888:8888 openvibspec/anaconda3
You'll be placed inside your instanciated docker container like so:
(py38) localuser@8087de7548e8:~$
If not already added, you should add your local notebook directory e.g. C:\Users\user\notebooks to the File Sharing section inside of your docker-widget settings. (Settings - Resources - File Sharing)
Afterwards you can run the following command:
docker run -it -v "C:\Users\user\notebooks:/opt/notebooks" -p 8888:8888 openvibspec/anaconda3
Due to the inability of docker-containers not running graphical interfaces directly, the invocation of jupyter notebook needs some arguments:
(py38) localuser@8087de7548e8:~$ jupyter notebook --ip="*" --no-browser --notebook-dir=/opt/notebooks
The notebook start should look like this in the shell:
[I 09:22:33.052 NotebookApp] Jupyter Notebook 6.4.0 is running at:
[I 09:22:33.052 NotebookApp] http://8087de7548e8:8888/?token=c061d3ebe26dbcc83bd661740b6e2fee3d8c84373fafa3f5
[I 09:22:33.052 NotebookApp] or http://127.0.0.1:8888/?token=c061d3ebe26dbcc83bd661740b6e2fee3d8c84373fafa3f5
[I 09:22:33.052 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 09:22:33.054 NotebookApp]
To access the notebook, open this file in a browser:
file:///home/localuser/.local/share/jupyter/runtime/nbserver-25-open.html
Or copy and paste one of these URLs:
http://8087de7548e8:8888/?token=c061d3ebe26dbcc83bd661740b6e2fee3d8c84373fafa3f5
or http://127.0.0.1:8888/?token=c061d3ebe26dbcc83bd661740b6e2fee3d8c84373fafa3f5
You have to manually copy the last line to your address-bar of your preferred browser:
http://127.0.0.1:8888/?token=c061d3ebe26dbcc83bd661740b6e2fee3d8c84373fafa3f5
The provided anaconda environment can be used to run OpenVibSpec. This environment is also preconfigured in the Docker images (see above).
You can use the yaml file in the repository root to set up a local, compatible anaconda environment.
Alternatively, you set up a virtual Python 3.6 environment manually. Use this as a reference of required libraries:
# packages in environment at xxx/envs/python36:
#
_tflow_select 2.1.0 gpu anaconda
absl-py 0.8.1 py36_0 anaconda
astor 0.8.0 py36_0 anaconda
backports 1.0 py36_0
backports.weakref 1.0rc1 py36_0
blas 1.0 mkl anaconda
bleach 1.5.0 py36_0
c-ares 1.15.0 h7b6447c_1001 anaconda
ca-certificates 2019.11.27 0 anaconda
cudatoolkit 10.0.130 0 anaconda
cudnn 7.6.5 cuda10.0_0 anaconda
cupti 10.0.130 0 anaconda
cycler 0.10.0 py36_0
dbus 1.10.22 h3b5a359_0 anaconda
decorator 4.0.11 py36_0
entrypoints 0.2.2 py36_1
enum34 1.1.6 <pip>
expat 2.1.0 0
fontconfig 2.12.4 h88586e7_1 anaconda
freetype 2.8 h52ed37b_0 anaconda
future 0.16.0 py36_1
gast 0.2.2 py36_0 anaconda
glib 2.53.6 hc861d11_1 anaconda
google-pasta 0.1.8 py_0 anaconda
grpcio 1.14.1 py36h9ba97e2_0 anaconda
gst-plugins-base 1.12.4 h33fb286_0 anaconda
gstreamer 1.12.4 hb53b477_0 anaconda
h5py 2.9.0 py36h7918eee_0 anaconda
hdf5 1.10.4 hb1b8bf9_0 anaconda
html5lib 0.9999999 py36_0
icu 58.2 h211956c_0 anaconda
intel-openmp 2019.5 281 anaconda
ipykernel 4.6.1 py36_0
ipython 6.1.0 py36_0
ipython_genutils 0.2.0 py36_0
ipywidgets 6.0.0 py36_0
jbig 2.1 0
jedi 0.10.2 py36_2
jinja2 2.9.6 py36_0
joblib 0.14.1 py_0 anaconda
jpeg 9b 0
jsonschema 2.6.0 py36_0
jupyter 1.0.0 py36_3
jupyter_client 5.1.0 py36_0
jupyter_console 5.1.0 py36_0
jupyter_core 4.3.0 py36_0
keras 2.1.6 py36_0 conda-forge
keras-applications 1.0.8 py_0 anaconda
keras-base 2.2.4 py36_0 anaconda
keras-preprocessing 1.1.0 py_1 anaconda
kiwisolver 1.1.0 py36he6710b0_0 anaconda
libedit 3.1.20181209 hc058e9b_0 anaconda
libffi 3.2.1 1
libgcc 7.2.0 h69d50b8_2 anaconda
libgcc-ng 9.1.0 hdf63c60_0 anaconda
libgfortran 3.0.0 1
libgfortran-ng 7.3.0 hdf63c60_0 anaconda
libgpuarray 0.6.8 0
libiconv 1.14 0
libpng 1.6.37 hbc83047_0 anaconda
libprotobuf 3.11.2 hd408876_0 anaconda
libsodium 1.0.10 0
libstdcxx-ng 9.1.0 hdf63c60_0 anaconda
libtiff 4.1.0 h2733197_0 anaconda
libxcb 1.12 1
libxml2 2.9.4 0
mako 1.0.6 py36_0
markdown 3.1.1 py36_0 anaconda
markupsafe 0.23 py36_2
matplotlib 2.2.2 py36h0e671d2_0 anaconda
mistune 0.7.4 py36_0
mkl 2019.5 281 anaconda
mkl-service 2.3.0 py36he904b0f_0 anaconda
mkl_fft 1.0.15 py36ha843d7b_0 anaconda
mkl_random 1.1.0 py36hd6b4f25_0 anaconda
nbconvert 5.2.1 py36_0
nbformat 4.3.0 py36_0
ncurses 6.1 he6710b0_1 anaconda
nose 1.3.7 py36_1
notebook 5.0.0 py36_0
numpy 1.17.4 py36hc1035e2_0 anaconda
numpy 1.13.0 <pip>
numpy-base 1.17.4 py36hde5b4d6_0 anaconda
olefile 0.44 py36_0
openssl 1.0.2u h7b6447c_0 anaconda
opt_einsum 3.1.0 py_0 anaconda
pandocfilters 1.4.1 py36_0
path.py 10.3.1 py36_0
pcre 8.39 1
pexpect 4.2.1 py36_0
pickleshare 0.7.4 py36_0
pillow 5.1.0 py36h3deb7b8_0 anaconda
pip 19.3.1 <pip>
pip 9.0.1 py36_1
prompt_toolkit 1.0.14 py36_0
protobuf 3.11.2 py36he6710b0_0 anaconda
ptyprocess 0.5.1 py36_0
pygments 2.2.0 py36_0
pygpu 0.6.8 py36_0
pyparsing 2.1.4 py36_0
pyqt 5.6.0 py36_2
python 3.6.6 h6e4f718_2 anaconda
python-dateutil 2.6.0 py36_0
pytz 2017.2 py36_0
pyyaml 5.2 py36h7b6447c_0 anaconda
pyzmq 16.0.2 py36_0
qt 5.6.2 h974d657_12 anaconda
qtconsole 4.3.0 py36_0
readline 7.0 h7b6447c_5 anaconda
scikit-learn 0.22.1 <pip>
scikit-learn 0.22 py36hd81dba3_0 anaconda
scipy 1.3.2 py36h7c811a0_0 anaconda
scipy 0.19.1 <pip>
setuptools 27.2.0 py36_0
simplegeneric 0.8.1 py36_1
sip 4.18 py36_0
six 1.10.0 <pip>
six 1.13.0 py36_0 anaconda
sqlite 3.30.1 h7b6447c_0 anaconda
tensorboard 1.6.0 py36_0 conda-forge
tensorboard 1.7.0 <pip>
tensorflow 1.6.0 py36_0 conda-forge
tensorflow-base 2.0.0 gpu_py36h0ec5d1f_0 anaconda
tensorflow-estimator 2.0.0 pyh2649769_0 anaconda
tensorflow-tensorboard 0.4.0 <pip>
tensorflow-tensorboard 0.1.5 py36_0
termcolor 1.1.0 py36_1 anaconda
terminado 0.6 py36_0
testpath 0.3.1 py36_0
Theano 0.9.0 <pip>
theano 0.9.0 py36_3 conda-forge
tk 8.6.8 hbc83047_0 anaconda
tornado 4.5.1 py36_0
traitlets 4.3.2 py36_0
wcwidth 0.1.7 py36_0
webencodings 0.5.1 py36h800622e_1 anaconda
werkzeug 0.16.0 py_0 anaconda
wheel 0.29.0 py36_0
widgetsnbextension 2.0.0 py36_0
wrapt 1.11.2 py36h7b6447c_0 anaconda
xz 5.2.4 h14c3975_4 anaconda
yaml 0.1.7 h96e3832_1 anaconda
zeromq 4.1.5 0
zlib 1.2.11 h7b6447c_3 anaconda
zstd 1.3.7 h0b5b093_0 anaconda
Correspondence:
Prof. Dr. Axel Mosig, Bioinformatics Group, Ruhr Universität Bochum, Germany
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