Commit eb951a1a authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

Update project.xml

parent f014a333
...@@ -3,16 +3,13 @@ ...@@ -3,16 +3,13 @@
<property name="common.os.prefix" value="common"/> <property name="common.os.prefix" value="common"/>
<sources> <sources>
<source name="LegioParis-chromosome-fasta" type="fasta">
<!-- 1 Legio paris -->
<source name="LegioParis-chromosome-fasta" type="fasta" dump="true">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Paris chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Paris chromosome sequence"/>
<property name="fasta.taxonId" value="297246"/> <property name="fasta.taxonId" value="297246"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/>
</source> </source>
<source name="LegioParis-gff" type="gff"> <source name="LegioParis-gff" type="gff">
...@@ -25,7 +22,17 @@ ...@@ -25,7 +22,17 @@
</source> </source>
<!-- <source name="Lfallonii-chromosome-fasta" type="fasta"> <source name="LegioParis-uniprot" type="uniprot">
<property name="uniprot.organisms" value="297246"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/uniprot"/>
<property name="creatego" value="true"/>
<property name="creategenes" value="true"/>
<property name="allowduplicates" value="false"/>
<property name="loadfragments" value="false"/>
<property name="loadtrembl" value="true"/>
</source>
<source name="Lfallonii-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella fallonii chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella fallonii chromosome sequence"/>
...@@ -43,9 +50,19 @@ ...@@ -43,9 +50,19 @@
<property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lfallonii"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lfallonii"/>
</source> </source>
-->
<!-- <source name="Lfallonii-uniprot" type="uniprot">
<property name="uniprot.organisms" value="96230"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/uniprot"/>
<property name="creatego" value="true"/>
<property name="creategenes" value="true"/>
<property name="allowduplicates" value="false"/>
<property name="loadfragments" value="false"/>
<property name="loadtrembl" value="true"/>
</source>
<source name="Lhackeliae-chromosome-fasta" type="fasta"> <source name="Lhackeliae-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
...@@ -64,9 +81,9 @@ ...@@ -64,9 +81,9 @@
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lhackeliae"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lhackeliae"/>
</source> </source>
-->
<!--
<source name="Lmicadei-chromosome-fasta" type="fasta"> <source name="Lmicadei-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
...@@ -85,10 +102,10 @@ ...@@ -85,10 +102,10 @@
<property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lmicadei"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lmicadei"/>
</source> </source>
-->
<!-- <source name="Long_Mage-chromosome-fasta" type="fasta">
<source name="Long_Mage-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella longbeachae NSW150 chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella longbeachae NSW150 chromosome sequence"/>
...@@ -105,12 +122,11 @@ ...@@ -105,12 +122,11 @@
<property name="gff3.seqClsName" value="Chromosome"/> <property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella longbeachae NSW150 genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella longbeachae NSW150 genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Long_Mage"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Long_Mage"/>
</source> --> </source>
<!-- pneumophila Lorraine --> <source name="lorraine-chromosome-fasta" type="fasta">
<!-- <source name="lorraine-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine chromosome sequence"/>
...@@ -127,15 +143,10 @@ ...@@ -127,15 +143,10 @@
<property name="gff3.seqClsName" value="Chromosome"/> <property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Lorraine genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Lorraine genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lorraine"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lorraine"/>
</source> --> </source>
<!-- Legionella pneumophila 2300/99 Alcoy -->
<!-- <source name="LpAlcoy-chromosome-fasta" type="fasta"> <source name="LpAlcoy-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila 2300/99 Alcoy chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila 2300/99 Alcoy chromosome sequence"/>
...@@ -152,11 +163,10 @@ ...@@ -152,11 +163,10 @@
<property name="gff3.seqClsName" value="Chromosome"/> <property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila 2300/99 Alcoy genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella pneumophila 2300/99 Alcoy genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpAlcoy"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpAlcoy"/>
</source> --> </source>
<!-- pneumophila Corby --> <source name="LpCorby-chromosome-fasta" type="fasta">
<!-- <source name="LpCorby-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Corby chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Corby chromosome sequence"/>
...@@ -174,13 +184,10 @@ ...@@ -174,13 +184,10 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Corby genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella pneumophila str. Corby genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpCorby"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpCorby"/>
</source> </source>
-->
<!-- Legionella pneumophila str. Lens -->
<!--
<source name="LpLens-chromosome-fasta" type="fasta"> <source name="LpLens-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
...@@ -199,10 +206,7 @@ ...@@ -199,10 +206,7 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Lens genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella pneumophila str. Lens genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpLens"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpLens"/>
</source> </source>
-->
<!-- Legionella pneumophila subsp. pneumophila str. Philadelphia 1 -->
<!--
<source name="LpPhila-chromosome-fasta" type="fasta"> <source name="LpPhila-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
...@@ -220,20 +224,37 @@ ...@@ -220,20 +224,37 @@
<property name="gff3.seqClsName" value="Chromosome"/> <property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Philadelphia 1 genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Philadelphia 1 genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpPhila"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpPhila"/>
</source> --> </source>
<source name="legiolist-homology" type="legiolist-homology">
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/"/>
<property name="src.data.dir.includes" value="table_orthos.txt"/>
<!-- taxids of the legio strain for each column -->
<property name="legiolistTaxids" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
</source>
<source name="entrez-organism" type="entrez-organism"> <source name="entrez-organism" type="entrez-organism">
<property name="src.data.file" location="organisms.xml"/> <property name="src.data.file" location="organisms.xml"/>
</source> </source>
<source name="so" type="so">
<property name="src.data.file" location="so.obo" />
<property name="licence" value="https://creativecommons.org/licenses/by/4.0/"/>
</source>
<source name="pubmed-gene" type="pubmed-gene">
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/publication"/>
<property name="pubmed.organisms" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
<property name="src.data.dir.includes" value="gene2pubmed"/>
</source>
</sources> </sources>
<post-processing> <post-processing>
<post-process name="create-references"/> <post-process name="create-references"/>
<post-process name="transfer-sequences" dump="true"/> <post-process name="transfer-sequences"/>
<post-process name="create-chromosome-locations-and-lengths"/> <post-process name="create-chromosome-locations-and-lengths"/>
<post-process name="transfer-sequences" dump="true"/>
<post-process name="do-sources" /> <post-process name="do-sources" />
<post-process name="create-attribute-indexes" /> <post-process name="create-attribute-indexes" />
<post-process name="create-search-index" /> <post-process name="create-search-index" />
......
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