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Gilligan Lab for Epidemiology and Modelling
Wheat rusts
ews-coordinator
Commits
611fc1ab
Commit
611fc1ab
authored
1 year ago
by
L. Bower
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updating docker
parent
deddb1cd
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configs/docker/build/Dockerfile
+16
-10
16 additions, 10 deletions
configs/docker/build/Dockerfile
configs/docker/run/launchDockerRunner_lb584_Local.sh
+3
-3
3 additions, 3 deletions
configs/docker/run/launchDockerRunner_lb584_Local.sh
with
19 additions
and
13 deletions
configs/docker/build/Dockerfile
+
16
−
10
View file @
611fc1ab
# syntax=docker/dockerfile:1
# syntax=docker/dockerfile:1
FROM
ubuntu:18.04
as
base_image
FROM
ubuntu:24.04
as
base_image
SHELL
["/bin/bash", "-c"]
#run mkdir as root
#run mkdir as root
RUN
mkdir
-p
/storage/app/EWS_prod/regions/EastAfrica/workspace
RUN
mkdir
-p
/storage/app/EWS_prod/regions/EastAfrica/workspace
...
@@ -10,10 +12,11 @@ WORKDIR /home
...
@@ -10,10 +12,11 @@ WORKDIR /home
#RUN mkdir /home/ewsmanager/code
#RUN mkdir /home/ewsmanager/code
#copy resources in
#copy resources in
COPY
./conda-env-py3EWS-nobuilds.yml .
#COPY ./conda-env-py3EWS-nobuilds.yml .
COPY
./requirements.txt .
#install system packages
#install system packages
RUN
apt-get update
;
apt-get
install
--assume-yes
wget unzip emacs gdal-bin libgdal-dev build-essential gfortran zlib1g zlib1g-dev libbz2-dev apt-utils liblzma-dev
libpcre++-dev
libcurl4-openssl-dev default-jre
lib32readline7 lib32readline6-dev
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
;
RUN
echo
"alias e='emacs -nw
$1
'"
>>
~/.bashrc
;
RUN
echo
"alias e='emacs -nw
$1
'"
>>
~/.bashrc
;
RUN
alias
ll
=
"ls -ltr"
RUN
alias
ll
=
"ls -ltr"
...
@@ -21,18 +24,21 @@ RUN alias ll="ls -ltr"
...
@@ -21,18 +24,21 @@ RUN alias ll="ls -ltr"
RUN
DEBIAN_FRONTEND
=
noninteractive
TZ
=
Etc/UTC apt-get
-y
install
tzdata
RUN
DEBIAN_FRONTEND
=
noninteractive
TZ
=
Etc/UTC apt-get
-y
install
tzdata
# Install miniconda
# Install miniconda
ENV
CONDA_DIR /storage/app/miniconda3
#
ENV CONDA_DIR /storage/app/miniconda3
RUN
wget
--quiet
https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-O
~/miniconda.sh
\
#
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh \
&&
/bin/bash ~/miniconda.sh
-b
-p
$CONDA_DIR
\
#
&& /bin/bash ~/miniconda.sh -b -p $CONDA_DIR \
&&
rm
-v
~/miniconda.sh
;
#
&& rm -v ~/miniconda.sh;
# Put conda in path so we can use conda activate
# Put conda in path so we can use conda activate
ENV
PATH=$CONDA_DIR/bin:$PATH
#
ENV PATH=$CONDA_DIR/bin:$PATH
#build the conda env(s)
#build the conda env(s)
RUN
conda
env
create
--file
conda-env-py3EWS-nobuilds.yml
--prefix
/storage/app/EWS_prod/envs/conda/py3EWS
#RUN conda env create --file conda-env-py3EWS-nobuilds.yml --prefix /storage/app/EWS_prod/envs/conda/py3EWS
RUN
python3
-m
venv ews_prod
RUN
source
ews_prod/bin/activate
;
pip
install
-r
requirements.txt
#tidy
#tidy
RUN
rm
-v
conda-env-py3EWS-nobuilds.yml
;
#RUN rm -v conda-env-py3EWS-nobuilds.yml;
#RUN rm -v requirements.txt;
#these usernames and ids match the production server (IaaS), override when building a local image if needed
#these usernames and ids match the production server (IaaS), override when building a local image if needed
ARG
GNAME=ews
ARG
GNAME=ews
...
...
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configs/docker/run/launchDockerRunner_lb584_Local.sh
+
3
−
3
View file @
611fc1ab
#!/bin/bash
#!/bin/bash
set
-e
set
-e
docker run
-it
-v
"/media/scratch/lb584_scratch/projects/ews_
aws/ews_3
/code:/storage/app/EWS_prod/code"
\
docker run
-it
-v
"/media/scratch/lb584_scratch/projects/ews_
instructions
/code:/storage/app/EWS_prod/code"
\
-v
"/media/scratch/lb584_scratch/projects/ews_
aws/ews_3/
regions:/storage/app/EWS_prod/regions"
\
-v
"/media/scratch/lb584_scratch/projects/ews_
instructions
regions:/storage/app/EWS_prod/regions"
\
-v
"/media/scratch/lb584_scratch/projects/ews_
aws/ews_3
/envs/credentials:/storage/app/EWS_prod/envs/credentials"
\
-v
"/media/scratch/lb584_scratch/projects/ews_
instructions
/envs/credentials:/storage/app/EWS_prod/envs/credentials"
\
-w
"/storage/app/EWS_prod/code"
\
-w
"/storage/app/EWS_prod/code"
\
--name
ews_runner
\
--name
ews_runner
\
ews_coordinator
ews_coordinator
...
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