Skip to content

GitLab

Commit 882a1845 authored by Ronan Trepos's avatar Ronan Trepos
Browse files

remove docker and galaxy tool 

There are now parts of RECORD repository
parent 7dc23b27
Hide whitespace changes
Inline Side-by-side
siwaa_recipe/README.txt deleted 100644 → 0
View file @ 7dc23b27
## build the docker image
docker build -t rtrepos/azodyn_pea:test container
## list images
docker images
## run image
docker run rtrepos/azodyn_pea:test ls
docker run -it rtrepos/azodyn_pea:test R #ouvre session R
### push image on docker hub
docker login
# pusher pour la production
docker push rtrepos/azodyn_pea:prod
#pusher pour les test (avec planemo)
docker push rtrepos/azodyn_pea:test
## run image with climate outside
cp ../AZODYN/data/Breteniere_1991_2018.csv Breteniere_1991_2018_test.csv
docker run -v $PWD:/work rtrepos/azodyn_pea /bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R /work/file_input.csv /work/file_output.csv 3 > razodyn.txt"
# with singularity
cp ../AZODYN/data/Breteniere_1991_2018.csv Breteniere_1991_2018_test.csv
singularity exec --cleanenv -B $PWD:/work docker://rtrepos/azodyn_pea:prod /bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R /work/file_input.csv /work/file_output.csv 3 > /work/razodyn.txt"
# with singularity without mounted PWD
singularity exec docker://rtrepos/azodyn_pea:test /bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R file_input.csv file_output.csv 5"
####planemo
cd galaxy_tools ;
planemo serve --job_config_file ../job_conf.xml tools_AZODYN.xml
## publish on toolshed
planemo shed_create --shed_target "http://147.100.179.176:9009/" --shed_email "siwaa@inra.fr" --shed_password "<TODO>"
siwaa_recipe/container/Dockerfile deleted 100644 → 0
View file @ 7dc23b27
FROM debian:buster-slim
RUN env \
&& apt-get update \
&& apt-get install --no-install-recommends --no-install-suggests -y \
curl git libexpat1 libexpat1-dev expat libboost-dev make cmake pkg-config g++ asciidoctor ruby-asciidoctor ninja-build libopenmpi-dev libopenmpi3 zip unzip\
r-base\
&& rm -rf /var/lib/apt/lists/*
ENV VLE_HOME=/data
WORKDIR /data
RUN git clone https://github.com/rtrepos/vle.git \
&& cd vle \
&& git checkout origin/manager -b manager \
&& mkdir build \
&& cd build \
&& cmake -G "Ninja" -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=RelWithDebInfo -DWITH_CVLE=ON -DWITH_GVLE=OFF .. \
&& ninja \
&& ninja install \
&& vle-2.1 --restart \
&& ctest --output-on-failure \
&& rm -fr build
RUN R --vanilla -e 'install.packages("RUnit", repos="http://cran.us.r-project.org")'
RUN R --vanilla -e 'install.packages("ggplot2", repos="http://cran.us.r-project.org")'
RUN R --vanilla -e 'install.packages("gridExtra", repos="http://cran.us.r-project.org")'
RUN R --vanilla -e 'install.packages("reshape2", repos="http://cran.us.r-project.org")'
RUN git clone https://github.com/rtrepos/rvle.git \
&& cd rvle \
&& git checkout origin/manager -b manager
RUN tar cfz rvle.tar.gz rvle \
&& rm -rf rvle
RUN R CMD INSTALL rvle.tar.gz
RUN git clone https://github.com/rtrepos/packages.git \
&& cd packages \
&& git checkout origin/manager -b manager
RUN cd packages \
&& vle -P vle.reader clean rclean configure build \
&& vle -P vle.tester clean rclean configure build \
&& vle -P vle.discrete-time clean rclean configure build
RUN git clone https://forgemia.inra.fr/record/RECORD.git \
&& cd RECORD \
&& git checkout origin/manager -b manager
RUN cd RECORD/pkgs \
&& vle -P record.meteo clean rclean configure build \
&& vle -P record.meteo_test clean rclean configure build test\
&& vle -P vle.discrete-time.generic clean rclean configure build
RUN git clone https://forgemia.inra.fr/record/azodyn.git \
&& cd azodyn \
&& git checkout origin/siwaa -b siwaa \
&& vle -P AZODYN configure build
RUN chmod -R 755 /data/vle-2001
WORKDIR /work
siwaa_recipe/file_input.csv deleted 100644 → 0
View file @ 7dc23b27
cPlant.coef_tot_a;condClimate.meteo_file
1.25;Breteniere_1991_2018_test.csv
1.5;Breteniere_1991_2018_test.csv
1.0;Breteniere_1991_2018_test.csv
1.25;Breteniere_1991_2018_test.csv
siwaa_recipe/galaxy_tools/.shed.yml deleted 100644 → 0
View file @ 7dc23b27
categories: [AgroEcosystems]
description: AzodynPea experiment plan simulation
name: azodyn_pea
owner: siwaa
siwaa_recipe/galaxy_tools/siwaa_macros.xml deleted 100644 → 0
View file @ 7dc23b27
<macros>
<xml name="slurm_task_account">
<section name="slurmadv" title="Advanced Options for Slurm" expanded="false">
<param name="account" type="text" value="record" label="Slurm account name" />
<param name="ntasks" type="integer" value="5" min="5" max="5" label="Slurm number of tasks" />
</section>
</xml>
<xml name="slurm_account">
<section name="slurmadv" title="Advanced Options for Slurm" expanded="false">
<param name="account" type="text" value="record" label="Slurm account name" />
</section>
</xml>
</macros>
siwaa_recipe/galaxy_tools/tools_AZODYN.xml deleted 100644 → 0
View file @ 7dc23b27
<tool id="AzodynPea" name="AzodynPea experiment plan simulation" version="1.0.0">
<description></description>
<requirements>
<container type="singularity">docker://rtrepos/azodyn_pea:prod</container>
</requirements>
<command detect_errors="aggressive">
unzip ${input_meteo};
/bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R ${file_input} ${file_outputs} 5";
zip temp_results.zip azodyn_plot.png azodyn_results_*.txt;
cp temp_results.zip ${azodyn_results};
</command>
<macros>
<import>siwaa_macros.xml</import>
</macros>
<inputs>
<param name="input_meteo" type="data" format="zip" label="input meteo (zip file)"/>
<param name="file_input" type="data" format="csv" label="azodyn inputs"/>
<param name="file_outputs" type="data" format="csv" label="azodyn outputs"/>
<expand macro="slurm_task_account" />
</inputs>
<outputs>
<data format="zip" name="azodyn_results" />
</outputs>
<help>
input meteo zip containing eg:
==============================
meteo1.csv and meteo2.csv
AZODYN inputs eg:
=================
cPlant.coef_tot_a;condClimate.meteo_file
1.25;meteo1.csv
1.5;meteo1.csv
1.0;meteo2.csv
1.25;meteo2.csv
AZODYN outputs eg:
==================
id;path;integration
"LAI";"view/AzodynPea:PlantGrowthPea.LAI";"all"
</help>
</tool>
siwaa_recipe/job_conf.xml deleted 100644 → 0
View file @ 7dc23b27
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
</plugins>
<destinations>
<destination id="local" runner="local">
<param id="singularity_enabled">true</param>
</destination>
</destinations>
</job_conf>
siwaa_recipe/razodyn.R deleted 100644 → 0
View file @ 7dc23b27
##
# Rscript --verbose razodyn.R file_input.csv file_output.csv 5 > razodyn.txt
##
print(Sys.info())
Sys.setenv(VLE_HOME = "/data")
file_define = "file_define.csv";
file_propagate = "file_propagate.csv";
file_replicate = "file_replicate.csv";
file_input = "file_input.csv";
file_output = "file_output.csv";
nbslots = 5
###config from args
args=(commandArgs(TRUE))
file_input = as.character(args[1]);
# # mycond1.myport1;mycond2.myport2;;mycond3.myport3
# 2.5;coucou;4
# 2.6;bye;1
# 2.4;pffff;6
file_output = args[2];
# #id of output, path, integration, aggregation_replicate, aggregation_input, replicate_quantile, time1, obs1, time2, obs2, ...
# myid1;myview/atomic.Port1;"last";"quantile";"all";0.2;123;0.5;138;0.8
nbslots = as.integer(args[3])
##
library(rvle)
print(paste("getwd:",getwd()))
print(paste("dir(getwd()):",dir(getwd())))
f = rvle.open("AzodynPea.vpz", "AZODYN")
rvle.set_log_level(f, 7);
rvle.manager_set_config(vleObj=f, parallel_option = "cvle", nb_slots = nbslots,
simulation_spawn = F, rm_MPI_files = T,
generate_MPI_host = T, working_dir = getwd());
inputs = rvleExp.parseSim(file_sim=file_input, vleObj=f, skip=0)
rvle.plan_propagate(f, cond="condClimate", port="PkgName", val="")
outs = read.table(file_output, sep=";",header=T, stringsAsFactors=F)
for (i in 1:nrow(outs)) {
rvle.plan_output(vleObj=f, id=outs$id[i], path=outs$path[i],
integration=outs$integration[i])
}
res = rvle.plan_run(f)
for (i in 1:nrow(outs)) {
write.table(res[[outs$id[i]]], file=paste(sep="", 'azodyn_results_',outs$id[i],'.txt'),
row.names=F, col.names=F, sep=";")
}
png(filename="azodyn_plot.png", width = 1000, height = 1000)
rvleExp.plot(res)
dev.off()
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment