Voir la source de Discussion:Espace Interactions Arbres Microorganismes/Serveurs

==Protocole==
* définir la séquence d'appel (ci dessous)
* générer le serveur sur machine développement
* installer les pages wikis 
* installer les fichiers
* mettre à jour l'en-tête et la page serveur
* mettre à jour [[Modèle:Wicri Bois lien serveur]]
==Modèle de paramétrage==
===Sur machine locale (mac)===
<source>
cd $WICRI_ROOT/Bois/explor/Thaumatin.storage

NlmPubMedExplorCorpus  -d ThaumatinV1  \
          -q "thaumatin" -s 2000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration Thomatine"
</source>


<source>
NlmPubMedGetCorpusSize -q '"rust effector*"'

cd $WICRI_ROOT/Bois/explor/RustEffector.storage

NlmPubMedExplorCorpus  -d RustEffectorV1  \
          -q '"rust effector*"' -s 2000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les effecteurs de la rouille "
</source>


<source>
NlmPubMedGetCorpusSize -q phanerochaete

cd $WICRI_ROOT/Bois/explor/Phanerochaete.storage

NlmPubMedExplorCorpus  -d PhanerochaeteV1  \
          -q Phanerochaete -s 2000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur le phanerochaete"
</source>


<source>
NlmPubMedGetCorpusSize -q "white rot"

cd $WICRI_ROOT/Bois/explor/WhiteRot.storage

NlmPubMedExplorCorpus  -d WhiteRotV1  \
          -q "white rot" -s 4000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur la pourriture ligneuse"
</source>


<source>
NlmPubMedGetCorpusSize -q willow

cd $WICRI_ROOT/Bois/explor/Willow.storage

NlmPubMedExplorCorpus  -d WillowV1  \
          -q willow -s 5000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur le saule"
</source>
===Sur VM LorExplor===
<source>
NlmPubMedGetCorpusSize -q "phytophthora effector"


mkdir $WICRI_ROOT/Bois/explor/PhytophthoraEffector.storage

cd $WICRI_ROOT/Bois/explor/PhytophthoraEffector.storage

NlmPubMedExplorCorpus  -d "PhytophthoraEffectorV1"  \
          -q "phytophthora effector" -s 5000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les effecteurs du phytophthora"
</source>
===Retour machine locale===
<source>
NlmPubMedGetCorpusSize -q '"rust"[All Fields] AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields]) AND ("genome"[MeSH Terms] OR "genome"[All Fields] OR "genomes"[All Fields] OR "genome s"[All Fields] OR "genomically"[All Fields] OR "genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields])'

7974

mkdir $WICRI_ROOT/Bois/explor/RustFungiGenomicsV1.storage

cd $WICRI_ROOT/Bois/explor/RustFungiGenomicsV1.storage

NlmPubMedExplorCorpus  -d RustFungiGenomicsV1   \
          -q '"rust"[All Fields] AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields]) AND ("genome"[MeSH Terms] OR "genome"[All Fields] OR "genomes"[All Fields] OR "genome s"[All Fields] OR "genomically"[All Fields] OR "genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields])'   -s 8000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur la génomique des pucciniales"
</source>


<source>
NlmPubMedGetCorpusSize -d -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])'

1989

mkdir $WICRI_ROOT/Bois/explor/BiopestPeptid.storage

cd $WICRI_ROOT/Bois/explor//BiopestPeptid.storage

NlmPubMedExplorCorpus  -d BiopestPeptidV1  \
          -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])' -s 7000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les peptides biopesticides"
</source>


<source>
NlmPubMedGetCorpusSize -q '("rapamycin s"[All Fields] OR "rapamycine"[All Fields] OR "rapamycins"[All Fields] OR "sirolimus"[MeSH Terms] OR "sirolimus"[All Fields] OR "rapamycin"[All Fields]) AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields])'

6033

mkdir $WICRI_ROOT/Bois/explor/RapamycinFungus.storage

cd $WICRI_ROOT/Bois/explor/RapamycinFungus.storage

NlmPubMedExplorCorpus  -d RapamycinFungusV1  \
          -q '("rapamycin s"[All Fields] OR "rapamycine"[All Fields] OR "rapamycins"[All Fields] OR "sirolimus"[MeSH Terms] OR "sirolimus"[All Fields] OR "rapamycin"[All Fields]) AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields])' -s 3500    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur la rapamycine et les champignons"
</source>
===Volumétrie croissante===
;cas simple:
<source>
NlmPubMedGetCorpusSize -q "chloroplast plant redox"

mkdir $WICRI_ROOT/Bois/explor/ChloroPlantRedox.storage

cd $WICRI_ROOT/Bois/explor/ChloroPlantRedox.storage

NlmPubMedExplorCorpus  -d ChloroPlantRedoxV1   \
          -q "chloroplast plant redox" -s 250    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les chloroplastes dans l'oxydoréduction chez les plantes"
</source>

;cas complexe:réécriture de le requête
<source>
NlmPubMedGetCorpusSize -q '("plant s"[All Fields] OR "planted"[All Fields] OR "planting"[All Fields] OR "plantings"[All Fields] OR "plants"[MeSH Terms] OR "plants"[All Fields] OR "plant"[All Fields]) AND ("pathogen"[All Fields] OR "pathogen s"[All Fields] OR "pathogene"[All Fields] OR "pathogenes"[All Fields] OR "pathogenic"[All Fields] OR "pathogenically"[All Fields] OR "pathogenicities"[All Fields] OR "pathogenicity"[MeSH Subheading] OR "pathogenicity"[All Fields] OR "virulence"[MeSH Terms] OR "virulence"[All Fields] OR "pathogenity"[All Fields] OR "pathogenous"[All Fields] OR "pathogens"[All Fields]) AND ("transcriptom"[All Fields] OR "transcriptomal"[All Fields] OR "transcriptome"[MeSH Terms] OR "transcriptome"[All Fields] OR "transcriptomes"[All Fields] OR "transcriptomic"[All Fields] OR "transcriptomically"[All Fields] OR "transcriptomics"[All Fields])'

1029

mkdir $WICRI_ROOT/Bois/explor/PlantPathoTrans.storage

cd $WICRI_ROOT/Bois/explor/PlantPathoTrans.storage

NlmPubMedExplorCorpus  -d PlantPathoTransV1  \
          -q '("plant s"[All Fields] OR "planted"[All Fields] OR "planting"[All Fields] OR "plantings"[All Fields] OR "plants"[MeSH Terms] OR "plants"[All Fields] OR "plant"[All Fields]) AND ("pathogen"[All Fields] OR "pathogen s"[All Fields] OR "pathogene"[All Fields] OR "pathogenes"[All Fields] OR "pathogenic"[All Fields] OR "pathogenically"[All Fields] OR "pathogenicities"[All Fields] OR "pathogenicity"[MeSH Subheading] OR "pathogenicity"[All Fields] OR "virulence"[MeSH Terms] OR "virulence"[All Fields] OR "pathogenity"[All Fields] OR "pathogenous"[All Fields] OR "pathogens"[All Fields]) AND ("transcriptom"[All Fields] OR "transcriptomal"[All Fields] OR "transcriptome"[MeSH Terms] OR "transcriptome"[All Fields] OR "transcriptomes"[All Fields] OR "transcriptomic"[All Fields] OR "transcriptomically"[All Fields] OR "transcriptomics"[All Fields])' -s 200    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur le transcriptome phytopathogène"
</source>