Commit f4a8f4ce authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

docker data path

parent e870dfb8
......@@ -11,7 +11,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="LegioList Legionella pneumophila str. Paris genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/LegioParis_10-05-2012_LegioList/"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LegioParis_10-05-2012_LegioList/"/>
</source>
<source name="LegioParis-chromosome-fasta" type="fasta" version="4.1.1">
......@@ -19,14 +19,14 @@
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Paris chromosome sequence"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/>
</source>
<source name="LegioParis-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="297246"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LegioParis_10-05-2012_LegioList-prot-gene.tsv"/>
</source>
......@@ -40,7 +40,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -50,7 +50,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/Lfallonii"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lfallonii"/>
</source>
<source name="Lfallonii-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -58,13 +58,13 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella fallonii chromosome sequence"/>
<property name="fasta.taxonId" value="96230"/>
<property name="fasta.includes" value="Lfallonii.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lfallonii-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="96230"/>
<property name="legiolist-gene-prot.dataSetTitle" value="LegioList Legionella fallonii proteins"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Lfallonii-prot-gene.tsv"/>
</source>
......@@ -79,7 +79,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="Lfallonii.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
<source name="Lhackeliae-gff" type="legiolist-gff" version="4.1.1">
......@@ -88,7 +88,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella hackeliae genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/Lhackeliae"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lhackeliae"/>
</source>
<source name="Lhackeliae-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -96,12 +96,12 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella hackeliae chromosome sequence"/>
<property name="fasta.taxonId" value="449"/>
<property name="fasta.includes" value="Lhackeliae.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lhackeliae-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="449"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Lhackeliae-prot-gene.tsv"/>
</source>
......@@ -115,7 +115,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="Lhackeliae.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -130,7 +130,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/Lmicadei"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lmicadei"/>
</source>
<source name="Lmicadei-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -138,13 +138,13 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella micdadei chromosome sequence"/>
<property name="fasta.taxonId" value="451"/>
<property name="fasta.includes" value="Lmicadei.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lmicadei-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="451"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Lmicadei-prot-gene.tsv"/>
</source>
......@@ -158,7 +158,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="Lmicadei.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -170,7 +170,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella longbeachae NSW150 genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/Long_Mage"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Long_Mage"/>
</source>
<source name="Long_Mage-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -178,12 +178,12 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella longbeachae NSW150 chromosome sequence"/>
<property name="fasta.taxonId" value="661367"/>
<property name="fasta.includes" value="Long_Mage.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Long_Mage-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="661367"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Long_Mage-prot-gene.tsv"/>
</source>
......@@ -196,7 +196,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="Long_Mage.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -208,7 +208,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<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/pre-process-data/genome/gff/clean/Lorraine"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lorraine"/>
</source>
<source name="lorraine-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -216,14 +216,14 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine chromosome sequence"/>
<property name="fasta.taxonId" value="1046632"/>
<property name="fasta.includes" value="Lorraine.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lorraine-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="1046632"/>
<property name="legiolist-gene-prot.dataSetTitle" value="LegioList Lorraine proteins"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Lorraine-prot-gene.tsv"/>
</source>
......@@ -238,7 +238,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="Lorraine.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -252,7 +252,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila 2300/99 Alcoy genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/LpAlcoy"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpAlcoy"/>
</source>
<source name="LpAlcoy-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -260,13 +260,13 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila 2300/99 Alcoy chromosome sequence"/>
<property name="fasta.taxonId" value="423212"/>
<property name="fasta.includes" value="LpAlcoy.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="LpAlcoy-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="423212"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpAlcoy-prot-gene.tsv"/>
</source>
......@@ -280,7 +280,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="LpAlcoy.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -295,7 +295,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Corby genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/LpCorby"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpCorby"/>
</source>
<source name="LpCorby-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -303,13 +303,13 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Corby chromosome sequence"/>
<property name="fasta.taxonId" value="400673"/>
<property name="fasta.includes" value="LpCorby.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="LpCorby-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="400673"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpCorby-prot-gene.tsv"/>
</source>
......@@ -323,7 +323,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="LpCorby.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -338,7 +338,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Lens genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/gff/clean/LpLens"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpLens"/>
</source>
<source name="LpLens-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -346,12 +346,12 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Lens chromosome sequence"/>
<property name="fasta.taxonId" value="297245"/>
<property name="fasta.includes" value="LpLens.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="LpLens-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="297245"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpLens-prot-gene.tsv"/>
</source>
......@@ -365,7 +365,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="LpLens.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -376,7 +376,7 @@
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<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/pre-process-data/genome/gff/clean/LpPhila"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpPhila"/>
</source>
<source name="LpPhila-chromosome-fasta" type="fasta" version="4.1.1">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -384,12 +384,12 @@
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1 chromosome sequence"/>
<property name="fasta.taxonId" value="272624"/>
<property name="fasta.includes" value="LpPhila.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="LpPhila-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<property name="legiolist.taxid" value="272624"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpPhila-prot-gene.tsv"/>
</source>
......@@ -403,7 +403,7 @@
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.suffix" value="protein" />
<property name="fasta.includes" value="LpPhila.faa"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
......@@ -419,7 +419,7 @@
</source> -->
<source name="legiolist-homology" type="legiolist-homology" version="4.1.1">
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/"/>
<property name="src.data.dir.includes" value="table_orthos.txt"/>
<property name="legiolistTaxids" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
</source>
......@@ -434,12 +434,12 @@
</source>
<source name="go" type="go">
<property name="src.data.file" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data/go-basic.obo"/>
<property name="src.data.file" location="/home/intermine/intermine/data/pre-process-data/go-basic.obo"/>
</source>
<!-- <source name="pubmed-gene" type="pubmed-gene">
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/pre-process-data"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data"/>
<property name="pubmed.organisms" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
<property name="src.data.dir.includes" value="gene2pubmed"/>
</source> -->
......
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