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Commit bfbbe478 authored by L. Bower's avatar L. Bower
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doc work, adding new tppls to docker image

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configs/docker/build/Dockerfile
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......@@ -4,7 +4,7 @@ FROM ubuntu:24.04 as base_image
SHELL ["/bin/bash", "-c"]
#install system packages
RUN apt-get update;apt-get install --assume-yes python-dev-is-python3 python3-dev python3.11-venv wget unzip emacs gdal-bin libgdal-dev build-essential gfortran zlib1g zlib1g-dev libbz2-dev apt-utils liblzma-dev libcurl4-openssl-dev default-jre openssh-server libfribidi-dev libfontconfig1-dev libspatialindex-dev git;
RUN apt-get update;apt-get install --assume-yes python-dev-is-python3 python3-dev python3.11-venv wget unzip emacs gdal-bin libgdal-dev build-essential gfortran zlib1g zlib1g-dev libbz2-dev apt-utils liblzma-dev libcurl4-openssl-dev default-jre openssh-server libfribidi-dev libfontconfig1-dev libspatialindex-dev git dos2unix nano;
#sets the timezone to London
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata
......
docs/_source/installation.rst
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......@@ -64,7 +64,7 @@ cd into <install_location>/code
.. code-block:: bash
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
or generate this string in bash:
......@@ -76,7 +76,6 @@ or generate this string in bash:
ews-plotting,plotting \
ews-epidemiology,epimodel \
ews-source-calculation,source_gen \
ews-coordinator,coordinator \
ews-job-flagging,flagdir \
ews-met-processing,met_extractor_v2 \
ews-postprocessing,post_processing;
......@@ -86,7 +85,7 @@ or generate this string in bash:
printf "%s" "git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/${repo}.git ${folder};"
done
:download:`Download .cmd file <../_static/assets/windows_clone_git.batch>`
:download:`Download .cmd file <../_static/assets/windows_clone_git.cmd>`
:download:`Download .sh file <../_static/assets/linux_clone_git.sh>`
......@@ -97,13 +96,20 @@ or generate this string in bash:
Due to the size, project resources are not included in the git repository. You will need to ask the Cambridge team
for the latest version of the resources archive.
.. admonition:: Add resources for one region at a time
There is a seperate resources archive for each geographic region. Currently there are two regions, EastAfrica and
SouthAsia. The instructions below denote the different regions with <EastAfrica/SouthAsia>. We suggest you start
with EastAfrica and get that working before setting up other regions.
Once you have received an archive of ``<EastAfrica/SouthAsia>_resources_<latest_date>.tar.gz`` from Cambridge, unpack
into ``<install_location>/regions/<EastAfrica/SouthAsia>/resources``. This will place all the necessary JSON
configuration and other assets required for the pipeline to run.
e.g.:
.. code-block:: bash
tar -zxvf resources_<latest_date>.tar.gz
cd <install_location>/regions/EastAfrica/resources
tar -zxvf eastafrica_resources_<latest_date>.tar.gz
Edit the coordinator run script to fix the root paths **(not necessary if running in our docker image)**:
......@@ -158,6 +164,7 @@ equivalent to place the conda dependencies in the same dir before running docker
bash build.sh
**building docker can take a while, typically 5-10 mins**
Make a copy of the docker launch template file and edit the source dir to match that of your installation.
......
docs/_static/assets/linux_clone_git.sh
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......@@ -5,7 +5,6 @@ git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
\ No newline at end of file
docs/_static/assets/windows_clone_git.batch → docs/_static/assets/windows_clone_git.cmd
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@ECHO OFF
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
\ No newline at end of file
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing
\ No newline at end of file
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