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CastronovaCastronova
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Merge pull request #29 from hydroshare/develop
Release 1.0
2 parents 3adc66f + 867cb7c commit bcb3c3b

32 files changed

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‎docker/Dockerfile

+8-147
Original file line numberDiff line numberDiff line change
@@ -1,153 +1,14 @@
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# Build as jupyterhub/singleuser
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# Run with the DockerSpawner in JupyterHub
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FROM castrona/hydroshare-jupyterhub:latest
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MAINTAINER Tony Castronova <acastronova@cuahsi.org>
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# Minimal Jupyter Notebook Stack comes with:
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# Jupyter Notebook 4.2.x
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# Conda Python 3.x
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# No preinstalled scientific computing packages
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# Unprivileged user jovyan (uid=1000, configurable, see options) in group users (gid=100) with ownership over /home/jovyan and /opt/conda
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# tini as the container entrypoint and start-notebook.sh as the default command
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# A start-singleuser.sh script for use as an alternate command that runs a single-user instance of the Notebook server, as required by JupyterHub
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# Options for HTTPS, password auth, and passwordless sudo
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######################################################
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### Begin - JupyterHub Development Image Additions ###
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######################################################
127

138

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FROM jupyter/scipy-notebook
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MAINTAINER Tony Castronova <tony.castronova@usu.edu>
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EXPOSE 8888
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USER root
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############################
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# INSTALL SYSTEM LIBRARIES #
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############################
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# libgeos-dev RHESYSS dependency
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# mpic++ TAUDEM dependency
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# libgdal-dev TAUDEM dependency
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# libproj-dev TAUDEM dependency
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RUN apt-get clean && apt-get update --fix-missing
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RUN apt-get install -y libgeos-dev mpic++ libproj-dev
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# install irods fuse
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RUN apt-get install -y fuse libfuse2 libfuse-dev
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RUN wget -q ftp://ftp.renci.org/pub/irods/releases/4.1.8/ubuntu12/irods-icommands-4.1.8-ubuntu12-x86_64.deb -O /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
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RUN dpkg -i /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
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RUN groupadd fuse && usermod -aG fuse jovyan
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RUN chmod g+rw /dev/fuse && chgrp fuse /dev/fuse
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# install rhessys workflows
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RUN apt-get install -y build-essential git subversion p7zip-full python python-dev python-pip python-scipy libxml2-dev libxslt-dev libgdal-dev libgdal-doc gdal-bin python-gdal grass grass-dev libbsd-dev vlc
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# create directories
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RUN mkdir /home/jovyan/libs && chown -R jovyan:users /home/jovyan/libs
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RUN mkdir /home/jovyan/work/notebooks && chown -R jovyan:users /home/jovyan/work/notebooks
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#RUN mkdir /home/jovyan/grassdata && chown -R jovyan:users /home/jovyan/grassdata
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###############################
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# SETUP JUPYTERHUB ENTRYPOINT #
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###############################
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# fetch juptyerhub-singleuser entrypoint
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RUN wget -q https://raw.githubusercontent.com/jupyterhub/jupyterhub/master/scripts/jupyterhub-singleuser -O /usr/local/bin/jupyterhub-singleuser && \
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chmod 755 /usr/local/bin/jupyterhub-singleuser
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ADD singleuser.sh /srv/singleuser/singleuser.sh
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# add grass create location script
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#RUN chmod 755 /home/jovyan/libs/create_grass_loc.sh && chown jovyan:users /home/jovyan/libs/create_grass_loc.sh
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# fetch the ecohydro config file
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ADD https://raw.githubusercontent.com/selimnairb/RHESSysWorkflows/master/docs/config/ecohydro-Linux.cfg /home/jovyan/.ecohydro.cfg
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RUN chown jovyan:users /home/jovyan/.ecohydro.cfg
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##################
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# PREPARE TAUDEM #
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##################
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# install taudem (must happend before rhesyss b/c of gdal conflicts)
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RUN git clone https://github.com/dtarb/TauDEM.git ../libs/TauDEM && \
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cd ../libs/TauDEM/src && make
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# link conda python2 (used by jupyterhub) to python22
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RUN ln -s /opt/conda/envs/python2/bin/python2 /usr/bin/python22
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# prepare grass
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#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
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#RUN chown jovyan:users /home/jovyan/libs/create_grass_loc.sh && \
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#chmod +x /home/jovyan/libs/create_grass_loc.sh
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#########################
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# SWITCH TO JOVYAN USER #
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#########################
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USER jovyan
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# load the rhessys configuration file
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RUN sed -i -e 's|^ETC.*|ETC = /home/jovyan/libs/RHESSysWorkflows/etc|g' /home/jovyan/.ecohydro.cfg &&\
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sed -i -e 's|^MODULE_PATH.*|MODULE_PATH = /home/jovyan/work/notebooks/.grass6/addons|g' /home/jovyan/.ecohydro.cfg &&\
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sed -i -e 's|^MODULE_ETC.*|MODULE_ETC = /home/jovyan/libs/RHESSysWorkflows/etc/r.soils.texture|g' /home/jovyan/.ecohydro.cfg
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# prepare python environments
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RUN pip install --upgrade pip
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# install ecohydrolib
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RUN git clone https://github.com/leonard-psu/EcohydroLib.git ../libs/EcohydroLib
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RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
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&& cd ../libs/EcohydroLib \
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&& python setup.py install "
99-
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# install RHESSysWorkflows
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RUN git clone https://github.com/leonard-psu/RHESSysWorkflows.git ../libs/RHESSysWorkflows
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RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
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&& cd ../libs/RHESSysWorkflows \
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&& python setup.py install"
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RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
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&& pip install --upgrade pip \
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&& pip install wget "
109-
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###############################
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# PREPARE PYTHON ENVIRONMENTS #
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###############################
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# Python 3
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RUN conda install -y -n root \
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gdal \
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basemap \
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landlab -c landlab
119-
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RUN git clone -b 2_and_3 https://github.com/hydroshare/hs_restclient.git ../libs/hs_restclient
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RUN /bin/bash -c "source /opt/conda/bin/activate root \
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&& cd ../libs/hs_restclient \
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&& python setup.py install "
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# Python 2
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# install gdal into python2 conda env
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RUN conda install -y -n python2 \
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gdal \
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basemap \
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landlab -c landlab
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######################
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# SET PATH VARIABLES #
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######################
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ENV PATH=/opt/conda/envs/python2/bin:/home/jovyan/libs/TauDEM:$PATH PYTHONPATH=/home/jovyan/work/notebooks/utilities:$PYTHONPATH DOCUMENTS=/home/jovyan/work/notebooks/documents DATA=/home/jovyan/work/notebooks/data HOME=/home/jovyan/work/notebooks ECOHYDROLIB_CFG=/home/jovyan/.ecohydro.cfg LD_LIBRARY_PATH=/usr/lib/grass64/lib
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#RUN /bin/bash -c "source /opt/conda/bin/activate python2" && \
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#pip install --upgrade hs_restclient
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# install odm2api, then upgrade it to renamevalueobjects branch
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RUN conda install -y -n python2 -c odm2 odm2api
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RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
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&& pip install --upgrade --process-dependency-links git+https://github.com/ODM2/ODM2PythonAPI.git@renamevalueobjects"
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# prepare grass environment
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#RUN mkdir notebooks
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#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
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ADD rhessys_wf.py /home/jovyan/libs/rhessys_wf.py
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ADD run.py /home/jovyan/libs/run.py
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###################################################
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## End - JupyterHub Development Image Additions ###
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###################################################
15112

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CMD ["sh", "/srv/singleuser/singleuser.sh"]
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‎docker/__init__.py

Whitespace-only changes.

‎docker/bck/Dockerfile

+155
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,155 @@
1+
# Build as jupyterhub/singleuser
2+
# Run with the DockerSpawner in JupyterHub
3+
4+
# Minimal Jupyter Notebook Stack comes with:
5+
# Jupyter Notebook 4.2.x
6+
# Conda Python 3.x
7+
# No preinstalled scientific computing packages
8+
# Unprivileged user jovyan (uid=1000, configurable, see options) in group users (gid=100) with ownership over /home/jovyan and /opt/conda
9+
# tini as the container entrypoint and start-notebook.sh as the default command
10+
# A start-singleuser.sh script for use as an alternate command that runs a single-user instance of the Notebook server, as required by JupyterHub
11+
# Options for HTTPS, password auth, and passwordless sudo
12+
13+
14+
FROM jupyter/scipy-notebook
15+
16+
MAINTAINER Tony Castronova <tony.castronova@usu.edu>
17+
18+
EXPOSE 8888
19+
20+
USER root
21+
22+
############################
23+
# INSTALL SYSTEM LIBRARIES #
24+
############################
25+
26+
# libgeos-dev RHESYSS dependency
27+
# mpic++ TAUDEM dependency
28+
# libgdal-dev TAUDEM dependency
29+
# libproj-dev TAUDEM dependency
30+
RUN apt-get clean && apt-get update --fix-missing
31+
32+
RUN apt-get install -y libgeos-dev mpic++ libproj-dev
33+
34+
# install irods fuse
35+
RUN apt-get install -y fuse libfuse2 libfuse-dev
36+
RUN wget -q ftp://ftp.renci.org/pub/irods/releases/4.1.8/ubuntu12/irods-icommands-4.1.8-ubuntu12-x86_64.deb -O /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
37+
RUN dpkg -i /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
38+
RUN groupadd fuse && usermod -aG fuse jovyan
39+
RUN chmod g+rw /dev/fuse && chgrp fuse /dev/fuse
40+
41+
# install rhessys workflows
42+
RUN apt-get install -y build-essential git subversion p7zip-full python python-dev python-pip python-scipy libxml2-dev libxslt-dev libgdal-dev libgdal-doc gdal-bin python-gdal grass grass-dev libbsd-dev vlc
43+
44+
# create directories
45+
RUN mkdir /home/jovyan/libs && chown -R jovyan:users /home/jovyan/libs
46+
RUN mkdir /home/jovyan/work/notebooks && chown -R jovyan:users /home/jovyan/work/notebooks
47+
#RUN mkdir /home/jovyan/grassdata && chown -R jovyan:users /home/jovyan/grassdata
48+
49+
###############################
50+
# SETUP JUPYTERHUB ENTRYPOINT #
51+
###############################
52+
53+
# fetch juptyerhub-singleuser entrypoint
54+
RUN wget -q https://raw.githubusercontent.com/jupyterhub/jupyterhub/master/scripts/jupyterhub-singleuser -O /usr/local/bin/jupyterhub-singleuser && \
55+
chmod 755 /usr/local/bin/jupyterhub-singleuser
56+
ADD singleuser.sh /srv/singleuser/singleuser.sh
57+
58+
# add grass create location script
59+
#RUN chmod 755 /home/jovyan/libs/create_grass_loc.sh && chown jovyan:users /home/jovyan/libs/create_grass_loc.sh
60+
61+
# fetch the ecohydro config file
62+
ADD https://raw.githubusercontent.com/selimnairb/RHESSysWorkflows/master/docs/config/ecohydro-Linux.cfg /home/jovyan/.ecohydro.cfg
63+
RUN chown jovyan:users /home/jovyan/.ecohydro.cfg
64+
65+
##################
66+
# PREPARE TAUDEM #
67+
##################
68+
69+
# install taudem (must happend before rhesyss b/c of gdal conflicts)
70+
RUN git clone https://github.com/dtarb/TauDEM.git ../libs/TauDEM && \
71+
cd ../libs/TauDEM/src && make
72+
73+
# link conda python2 (used by jupyterhub) to python22
74+
RUN ln -s /opt/conda/envs/python2/bin/python2 /usr/bin/python22
75+
76+
# prepare grass
77+
#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
78+
#RUN chown jovyan:users /home/jovyan/libs/create_grass_loc.sh && \
79+
#chmod +x /home/jovyan/libs/create_grass_loc.sh
80+
81+
#########################
82+
# SWITCH TO JOVYAN USER #
83+
#########################
84+
USER jovyan
85+
86+
# load the rhessys configuration file
87+
RUN sed -i -e 's|^ETC.*|ETC = /home/jovyan/libs/RHESSysWorkflows/etc|g' /home/jovyan/.ecohydro.cfg &&\
88+
sed -i -e 's|^MODULE_PATH.*|MODULE_PATH = /home/jovyan/work/notebooks/.grass6/addons|g' /home/jovyan/.ecohydro.cfg &&\
89+
sed -i -e 's|^MODULE_ETC.*|MODULE_ETC = /home/jovyan/libs/RHESSysWorkflows/etc/r.soils.texture|g' /home/jovyan/.ecohydro.cfg
90+
91+
# prepare python environments
92+
RUN pip install --upgrade pip
93+
94+
# install ecohydrolib
95+
RUN git clone https://github.com/leonard-psu/EcohydroLib.git ../libs/EcohydroLib
96+
RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
97+
&& cd ../libs/EcohydroLib \
98+
&& python setup.py install "
99+
100+
# install RHESSysWorkflows
101+
RUN git clone https://github.com/leonard-psu/RHESSysWorkflows.git ../libs/RHESSysWorkflows
102+
RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
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&& cd ../libs/RHESSysWorkflows \
104+
&& python setup.py install"
105+
106+
RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
107+
&& pip install --upgrade pip \
108+
&& pip install wget "
109+
110+
###############################
111+
# PREPARE PYTHON ENVIRONMENTS #
112+
###############################
113+
114+
# Python 3
115+
RUN conda install -y -n root \
116+
gdal \
117+
basemap \
118+
landlab -c landlab
119+
120+
RUN git clone -b 2_and_3 https://github.com/hydroshare/hs_restclient.git ../libs/hs_restclient
121+
RUN /bin/bash -c "source /opt/conda/bin/activate root \
122+
&& cd ../libs/hs_restclient \
123+
&& python setup.py install "
124+
125+
# Python 2
126+
# install gdal into python2 conda env
127+
RUN conda install -y -n python2 \
128+
gdal \
129+
basemap \
130+
landlab -c landlab
131+
132+
######################
133+
# SET PATH VARIABLES #
134+
######################
135+
136+
ENV PATH=/opt/conda/envs/python2/bin:/home/jovyan/libs/TauDEM:$PATH PYTHONPATH=/home/jovyan/work/notebooks/utilities:$PYTHONPATH DOCUMENTS=/home/jovyan/work/notebooks/documents DATA=/home/jovyan/work/notebooks/data HOME=/home/jovyan/work/notebooks ECOHYDROLIB_CFG=/home/jovyan/.ecohydro.cfg LD_LIBRARY_PATH=/usr/lib/grass64/lib
137+
138+
#RUN /bin/bash -c "source /opt/conda/bin/activate python2" && \
139+
#pip install --upgrade hs_restclient
140+
141+
# install odm2api, then upgrade it to renamevalueobjects branch
142+
RUN conda install -y -n python2 -c odm2 odm2api
143+
#RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
144+
#&& pip install --upgrade --process-dependency-links git+https://github.com/ODM2/ODM2PythonAPI.git@renamevalueobjects"
145+
146+
# prepare grass environment
147+
#RUN mkdir notebooks
148+
#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
149+
ADD rhessys_wf.py /home/jovyan/libs/rhessys_wf.py
150+
ADD run.py /home/jovyan/libs/run.py
151+
152+
CMD ["sh", "/srv/singleuser/singleuser.sh"]
153+
154+
155+

‎docker/cleanup.cron ‎docker/bck/cleanup.cron

File renamed without changes.

‎docker/create_grass_loc.sh ‎docker/bck/create_grass_loc.sh

File renamed without changes.

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