Commit 2e9d360f authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

Add version to source

parent 5fb40ecd
...@@ -5,7 +5,7 @@ ...@@ -5,7 +5,7 @@
<sources> <sources>
<!-- First gff and then fasta if you want to have the sequence available --> <!-- First gff and then fasta if you want to have the sequence available -->
<source name="LegioParis-gff" type="legiolist-gff"> <source name="LegioParis-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="297246"/> <property name="gff3.taxonId" value="297246"/>
<property name="gff3.seqDataSourceName" value="LegioList LegioParis"/> <property name="gff3.seqDataSourceName" value="LegioList LegioParis"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LegioParis_10-05-2012_LegioList/"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LegioParis_10-05-2012_LegioList/"/>
</source> </source>
<source name="LegioParis-chromosome-fasta" type="fasta"> <source name="LegioParis-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.taxonId" value="297246"/> <property name="fasta.taxonId" value="297246"/>
<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"/>
...@@ -24,14 +24,14 @@ ...@@ -24,14 +24,14 @@
</source> </source>
<source name="LegioParis-protein-gene" type="legiolist-gene-prot"> <source name="LegioParis-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="297246"/> <property name="legiolist.taxid" value="297246"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LegioParis_10-05-2012_LegioList-prot-gene.tsv"/> <property name="src.data.dir.includes" value="LegioParis_10-05-2012_LegioList-prot-gene.tsv"/>
</source> </source>
<source name="LegioParis-protein-fasta" type="fasta"> <source name="LegioParis-protein-fasta" type="fasta" version="4.1.1">
<property name="fasta.taxonId" value="297246"/> <property name="fasta.taxonId" value="297246"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/> <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/> <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
...@@ -64,7 +64,7 @@ ...@@ -64,7 +64,7 @@
--> -->
<source name="Lfallonii-gff" type="legiolist-gff"> <source name="Lfallonii-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="96230"/> <property name="gff3.taxonId" value="96230"/>
<property name="gff3.seqDataSourceName" value="LegioList Lfalloni"/> <property name="gff3.seqDataSourceName" value="LegioList Lfalloni"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -72,7 +72,7 @@ ...@@ -72,7 +72,7 @@
<property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lfallonii"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lfallonii"/>
</source> </source>
<source name="Lfallonii-chromosome-fasta" type="fasta"> <source name="Lfallonii-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
...@@ -81,7 +81,7 @@ ...@@ -81,7 +81,7 @@
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source> </source>
<source name="Lfallonii-protein-gene" type="legiolist-gene-prot"> <source name="Lfallonii-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="96230"/> <property name="legiolist.taxid" value="96230"/>
<property name="legiolist-gene-prot.dataSetTitle" value="LegioList Legionella fallonii proteins"/> <property name="legiolist-gene-prot.dataSetTitle" value="LegioList Legionella fallonii proteins"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/>
...@@ -89,7 +89,7 @@ ...@@ -89,7 +89,7 @@
</source> </source>
<source name="Lfallonii-protein-fasta" type="fasta"> <source name="Lfallonii-protein-fasta" type="fasta" version="4.1.1">
<property name="fasta.taxonId" value="96230"/> <property name="fasta.taxonId" value="96230"/>
<property name="fasta.dataSetTitle" value="Legiolist Lfallonii protein sequence"/> <property name="fasta.dataSetTitle" value="Legiolist Lfallonii protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/> <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
...@@ -102,7 +102,7 @@ ...@@ -102,7 +102,7 @@
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/>
</source> </source>
<source name="Lhackeliae-gff" type="legiolist-gff"> <source name="Lhackeliae-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="449"/> <property name="gff3.taxonId" value="449"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella hackeliae"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella hackeliae"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -110,7 +110,7 @@ ...@@ -110,7 +110,7 @@
<property name="gff3.dataSetTitle" value="Legionella hackeliae genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella hackeliae genome annotation"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lhackeliae"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lhackeliae"/>
</source> </source>
<source name="Lhackeliae-chromosome-fasta" type="fasta"> <source name="Lhackeliae-chromosome-fasta" type="fasta" version="4.1.1">
<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 hackeliae chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella hackeliae chromosome sequence"/>
...@@ -121,7 +121,7 @@ ...@@ -121,7 +121,7 @@
<source name="Lmicadei-gff" type="legiolist-gff"> <source name="Lmicadei-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="451"/> <property name="gff3.taxonId" value="451"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella micdadei"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella micdadei"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -129,7 +129,7 @@ ...@@ -129,7 +129,7 @@
<property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/> <property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lmicadei"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lmicadei"/>
</source> </source>
<source name="Lmicadei-chromosome-fasta" type="fasta"> <source name="Lmicadei-chromosome-fasta" type="fasta" version="4.1.1">
<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 micdadei chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella micdadei chromosome sequence"/>
...@@ -140,7 +140,7 @@ ...@@ -140,7 +140,7 @@
<source name="Long_Mage-gff" type="legiolist-gff"> <source name="Long_Mage-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="661367"/> <property name="gff3.taxonId" value="661367"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella longbeachae NSW150"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella longbeachae NSW150"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -148,7 +148,7 @@ ...@@ -148,7 +148,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Long_Mage"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Long_Mage"/>
</source> </source>
<source name="Long_Mage-chromosome-fasta" type="fasta"> <source name="Long_Mage-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
...@@ -160,7 +160,7 @@ ...@@ -160,7 +160,7 @@
<source name="Lorraine-gff" type="legiolist-gff"> <source name="Lorraine-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="1046632"/> <property name="gff3.taxonId" value="1046632"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -168,7 +168,7 @@ ...@@ -168,7 +168,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lorraine"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lorraine"/>
</source> </source>
<source name="lorraine-chromosome-fasta" type="fasta"> <source name="lorraine-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
...@@ -181,7 +181,7 @@ ...@@ -181,7 +181,7 @@
<source name="LpAlcoy-gff" type="legiolist-gff"> <source name="LpAlcoy-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="423212"/> <property name="gff3.taxonId" value="423212"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila 2300/99 Alcoy"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila 2300/99 Alcoy"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -189,7 +189,7 @@ ...@@ -189,7 +189,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpAlcoy"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpAlcoy"/>
</source> </source>
<source name="LpAlcoy-chromosome-fasta" type="fasta"> <source name="LpAlcoy-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
...@@ -201,7 +201,7 @@ ...@@ -201,7 +201,7 @@
<source name="LpCorby-gff" type="legiolist-gff"> <source name="LpCorby-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="400673"/> <property name="gff3.taxonId" value="400673"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Corby"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Corby"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -209,7 +209,7 @@ ...@@ -209,7 +209,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpCorby"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpCorby"/>
</source> </source>
<source name="LpCorby-chromosome-fasta" type="fasta"> <source name="LpCorby-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
...@@ -223,7 +223,7 @@ ...@@ -223,7 +223,7 @@
<source name="LpLens-gff" type="legiolist-gff"> <source name="LpLens-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="297245"/> <property name="gff3.taxonId" value="297245"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Lens"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Lens"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -231,7 +231,7 @@ ...@@ -231,7 +231,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpLens"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpLens"/>
</source> </source>
<source name="LpLens-chromosome-fasta" type="fasta"> <source name="LpLens-chromosome-fasta" type="fasta" version="4.1.1">
<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. Lens chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Lens chromosome sequence"/>
...@@ -242,7 +242,7 @@ ...@@ -242,7 +242,7 @@
<source name="LpPhila-gff" type="legiolist-gff"> <source name="LpPhila-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="272624"/> <property name="gff3.taxonId" value="272624"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1"/> <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1"/>
<property name="gff3.dataSourceName" value="LegioList"/> <property name="gff3.dataSourceName" value="LegioList"/>
...@@ -250,7 +250,7 @@ ...@@ -250,7 +250,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpPhila"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpPhila"/>
</source> </source>
<source name="LpPhila-chromosome-fasta" type="fasta"> <source name="LpPhila-chromosome-fasta" type="fasta" version="4.1.1">
<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. Philadelphia 1 chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1 chromosome sequence"/>
...@@ -269,7 +269,7 @@ ...@@ -269,7 +269,7 @@
<property name="loadtrembl" value="true"/> <property name="loadtrembl" value="true"/>
</source> --> </source> -->
<source name="legiolist-homology" type="legiolist-homology"> <source name="legiolist-homology" type="legiolist-homology" version="4.1.1">
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/"/> <property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/"/>
<property name="src.data.dir.includes" value="table_orthos.txt"/> <property name="src.data.dir.includes" value="table_orthos.txt"/>
<property name="legiolistTaxids" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/> <property name="legiolistTaxids" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
......
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