R PACKAGE DEVELOPMENT USING GITLAB CI/CD BUILD YOUR OWN PIPELINE

Many things to improve :

-Automate Virtual Machine creation and configuration -Use a local CRAN for auto delivery -Enable more GitLab fonctionnalities (web terminal, pages...

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  ) -Use Kubernetes (container orchestration) -CI/CD strategies "GitLab is a single application for the entire software development lifecycle. From project planning and source code management to CI/CD, monitoring, and security." (https://about.gitlab.com) • Community Edition (MIT licence) +free -features • Entreprise Edition (proprietary license) +features Our solution : -GitLab CE (on a server) -Gitlab-runner (on a server and desktop computer) https://gitlab.paca.inra.fr => R package development management tool -Multi-users and collaborative mode -Versioning (Git) -Private and public repositories -Self-hosted tools -Automate the maximum (save time) Docker Hub official images (r-base, r-devel...) GitLab Container Registry Custom docker images (r-base-biosp, r-devel-biosp…) Multiple OS and configuration constraints • Computer information system constraints • Check code regression • Code quality review and easy to deploy • Reproductibility -Most important : modern and simple to use (web interface)

Pipeline visualisation into GitLab

Nowadays computer project management tools are widely widespread, many of them provide a specific part of project life cycle management or are thirdparties solutions.

Here we introduce GitLab CE (Community Edition), an open core, free and full solution to manage R packages developments, delivery and many more. We focus in its Continuous Integration and Delivery pipeline part, using Docker and VirtualBox, for R packaging.

This local solution uses in our laboratory allows us to develop R codes in a collaborative mode and to automate R packages checking and building. This process allows us to share private and/or in development R packages on multiples OS and to accelerate CRAN submission by decreasing checking error.

PRESENTATION GITLAB NEEDS PIPELINE ARCHITECTURE

.gitlab-ci.yml GITLAB-RUNNER GO FURTHER


B Quilot

T Pascal

P Lambert

H Duval

J L Poëssel

M Corre

L Heurtevin

N Dlalah

C Tuero

V Signoret

V Decroocq

S Decroocq

D Tricon

Personnal involved in peach breeding for resistance-INRA-UGAFL

General Peach linkage map (8 chromosomes)

LG7 LG6 LG5 LG4

LG1

LG2

LG3

LG8

Vr1 or Vr2 R to powdery mildew Two phenolic compounds toxic for aphids identified

SD-PM.8.1 R to powdery mildew

Ppe-Xap-F6 R to Xanthomonas

•Dicaffeoylquinic acid (diCQ)

•Chicoric acid (diCT)

• A new patent granted for aphicide activity of diCT

• An ongoing contract with a private company to develop theses compounds as biopesticides (aphicide and fungicide)

• A start-up licensed for patent on diCQ production from plants Towards natural compounds, safe for human health and the environment, to control aphids

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  More restrictive standards and stronger limitations of the use of chemicals and pesticides in the European community 250 active phyto-sanitary substances forbidden in Europe to date • Increase of the consumer pressure for sustainable environment-friendly fruit production Responses of peach growers • General trend to reduce synthetic pesticides and fertilizers • Development of integrative cultural practices and alternative phyto-protection to limit their use • Slow but continuous development of Organic farming Response of researchers Researches aimed at developing resistant cultivars with good agronomical features for long-term sustainable sanitary protection International Workshop ORGANIST (Organic Farming Reasearch and Perspectives) Genetic control based on sources of resistance is natural and safe • Does not impact environment negatively • Could insure long-term sustainable sanitary protection of the orchards However • Need for sources of resistance covering a broad range of pests and pathogens systematic phenotyping of peach collections would allow uncovering new sources of resistance • Not or little taken into account by commercial breeders to date Need to be addressed by public Institutes International Workshop ORGANIST (Organic Farming Reasearch and Perspectives) identifying new genitors, sources of resistance or resilience combining several strong monogenic resistance factors in improved cultivars testing resistance durability in multi-site orchards and low-input conditions Long term : sustainable resistance by combining monogenic (Mendelian) and polygenic quantitative resistance factors to prevent resistance to be overcome, thanks to molecular markers • bi-parental progenies • populations segregating for multitraits interdependent populations • multi-parental populations • core-collections • Aphids, powdery mildew, bacterial spot, leaf curl, brown rot, sharka • root-knot nematodes (root-stocks) in conditions of low-input management Main targets to meet challenges Plant material 8 Our primary objective: improving resistance in peach International Workshop ORGANIST (Organic Farming Reasearch and Perspectives) Milan (Italie), 30 th May 2018 Contribute to the development of new methods for a sustainable, environment-friendly, peach orchard • by repositioning our team upstream of the peach breeding programs on objectives not/little taken into account by the others stakeholders • by transfering to breeders know-how, tools and improved material for the further development of full varietal ranges pre-breeding/elite material molecular marker linked to resistance characters DNA-informed methods for seedling selection International Workshop ORGANIST (Organic Farming Reasearch and Perspectives) resistant to powdery mildew, green peach aphid leaf curl and PPV … but the agronomical level is very low

International Workshop ORGANIST (Organic Farming Reasearch and Perspectives)Milan (Italie), 30 th May 2018

Prunus persica

Green

Powdery mildew + green peach aphid

• Improved genitors available but commercial agronomic value still to be improved

Leaf curl

• Genitors associating resistance regions evaluated , hybrids underway

Quantitative resistances derived from P. davidiana

• Individuals including several regions associated to resistance available for sustainable resistance program

Bacterial spot

• A project to select genitors using markers derived from RosBREED (https://www.rosbreed.org/) in association with French breeders underway

Nematodes + green peach aphid

• Individuals associating both resistance regions available (rootstock material)

• vector of viruses such as Plum Pox Virus, Sharka (quarantine disease)

• observed resistance to all pesticides

Agronomy

• a main threat for peach (Prunus persica) (primary host)

• and for many other crops as solanaceous vegetables (secondary hosts)

Example of outcome : the work on peach resistance to Myzus persicae

Myzus persicae


Loïc Francon

Thierry Ameglio

Erwan Roussel

Irène Till Bottraud

Guillaume Charrier

Christophe Corona

Wood formation in rhododendrons at the stress line: take a shrub to the limit

Keywords:

à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

June 2017: Heat wave for the rhodoendrons -Globally warm temperatures -Summer rain the 16th, the 26th and wet weather at the end of the month After a period directly afetr snowmelt when all individuals (Rf45 and Rf46) seem to lose water, they seem to recover in June.

Rf46 is growing (cambial innitiation about the 19th) whereas Rf45 does not make wood.

In this study, electronic micro-dendrometers were used to monitor the variations in stem diameter of 11 Rhododendron ferrugineum (Rf) individuals located at 1800, 2100 and 2500m asl in the Taillefer Massif (French Alps) and at 1700m asl at Vicdessos (French Pyrenees). In addition, ground-level temperature was recorded for each individual. The results presented here are focused on the 2500m site. They cover the period October 2016 -October 2017.

Context:

-High-latitude and high-altitude ecosystems are adapted to high level of environmental constraints and are therefore amongst the most sensitive to ongoing climate change. Numerous studies demonstrated that recent global warming leads to an increase in shrubs cover and productivity at the Arctic and Alpine treelines since the 1980s (ie 'shrubification').

-Dendroecological studies along an altitudinal gradient in the Taillefer massif (French Alps) reveal that R. ferrugineum growth was significantly and positively associated with May temperature and negatively correlated with winter precipitations at 2500m asl.

-Daily-resolved and homogeneized series of temperature, precipitation and snow cover depth from the SAFRAN-CROCUS datasets -for the period 1959-2016 -further confirm that both climatic parameters are the main drivers for snowmelt and subsequent growing season length at this altitude. -However, the dendroecological analyses that approximate relationships between tree rings and climate by a time-invariant function consider the underlying processes as a black-box (Guiot et al., 2014). In this context, the monitoring approach developed here is complementary to the correlation function analyses to document the ecophysiologixcal response of rhododendrons to meteorological/climatic fluctuations. At 1800m., during the growing season (summer 2016), we observe a typical growth curve. Growth, at this altitude stops by end August. This shows the potential of microdendrometers to track daily variations of diameter, growth and cambial innitiation of dwarf shrubs. Raw curves of diameters variations and temperatures are strongly snowpack-dependants. The gaps in the middle or at the end of the records corresponds to (1) loss of the signal or (2) abberant values due mechanical moving of the sensor.

In conclusion, our study demonstrates the complementarity of dendroecological and ecophysiological approaches to assess the response of shrub growth to (micro)climatic variability in alpine environments. The monitoring of dwarf shrubs at high altitude/latitude yet remains a technical and scientific challenge and further investigations are needed.

From a technical point of view, the main challenges are related to the improvement of the sensor reliability -electronic components and batteries -in extreme humidity and temperature conditions. Amongst the 11 microdendrometers installed at the different sites, only 5 operated for the winter, 4 ran out of battery and two lost the data before the end of the winter.

From a scientific point of view, we expect that our approach will permit to better assess the role of microclimatic fluctuations on the ecophysiology of alpine and arctic dwarf shrubs in the continuum ground-snowpack-plant-atmosphere.

Loïc Francon (1), Thierry Améglio (2), Erwan Roussel (1), Irène Till Bottraud (1), Guillaume Charrier (2) and Christophe Corona (1)

(1) Université Clermont Auvergne, CNRS, GEOLAB, F-63000 CLERMONT-FERRAND, France -Snowfalls the 27th. Rehydration of all stems

  temperature records (°C) Diameter of 1800m asl. site rhododendron individual stem (µm)

  try at 1800m in summer : the potential of microdendrometers on dwarf shrubs 3-One-year hourly monitoring of three rhododendrons shrubs stem diameter variations at 2500m asl.

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  2) Université Clermont Auvergne, INRA, PIAF, F-63000 CLERMONT-FERRAND, France contact: loic.francon@uca.fr No snowcover --> freeze/thaw cycles (beggining of the month) High amplitude contractions (125µm) -First snowfalls (13th and 14th) Rehydration of the stems -Warm temperatures during the day do not allow snowcover persistance (Only until the 19th). No snowcover --> freeze/thaw cycles (19th -24th) Moderate contractions -End October: positive temperatures (days and nights) Transpiration for all individuals April 2017: The week without snow -Warmer temperature and shallow snowpack lead to an exceptionnally early snowmelt. Individuals have to endure a prolonged period without protection against frost modulated by their microtopographic position. Rf46 undergoes the longest period. High amplitude contractions are observed for Rf46 and Rf45 -Sunny days and probably frozen soil Transpiration during the day -> Rf45 and Rf46 lose water.

Wood formation in rhododendrons at the stress line: Take a shrub to the limit