Commit c04ab37e authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

Update path to data in project

parent 9f0efcf3
......@@ -5,13 +5,13 @@
<sources>
<!-- First gff and then fasta if you want to have the sequence available -->
<source name="LegioParis-gff" type="legiolist-gff" version="4.1.1">
<!-- <source name="LegioParis-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="297246"/>
<property name="gff3.seqDataSourceName" value="LegioList LegioParis"/>
<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="/mnt/gaia/home/projects/legiolist/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="/mnt/gaia/home/projects/legiolist/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="/mnt/gaia/home/projects/legiolist/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>
......@@ -40,8 +40,8 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/protein"/>
</source>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source> -->
<!-- <source name="LegioParis-ncbi-gff" type="legiolist-gff">
......@@ -70,7 +70,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -78,13 +78,13 @@
<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="/mnt/gaia/home/projects/legiolist/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="/mnt/gaia/home/projects/legiolist/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>
......@@ -99,16 +99,16 @@
<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="/mnt/gaia/home/projects/legiolist/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">
<!-- <source name="Lhackeliae-gff" type="legiolist-gff" version="4.1.1">
<property name="gff3.taxonId" value="449"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella hackeliae"/>
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -116,7 +116,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -127,7 +127,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -135,7 +135,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -146,7 +146,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -154,7 +154,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -166,7 +166,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -174,7 +174,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -187,7 +187,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -195,7 +195,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -207,7 +207,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -215,7 +215,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -229,7 +229,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -237,7 +237,7 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
......@@ -248,7 +248,7 @@
<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="/mnt/gaia/home/projects/legiolist/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"/>
......@@ -256,8 +256,8 @@
<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="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source> -->
<!-- <source name="uniprot" type="uniprot">
<property name="uniprot.organisms" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
......@@ -269,11 +269,11 @@
<property name="loadtrembl" value="true"/>
</source> -->
<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/"/>
<!-- <source name="legiolist-homology" type="legiolist-homology" version="4.1.1">
<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>
</source> -->
<source name="entrez-organism" type="entrez-organism">
<property name="src.data.file" location="organisms.xml"/>
......@@ -285,12 +285,12 @@
</source>
<source name="go" type="go">
<property name="src.data.file" location="/mnt/gaia/home/projects/legiolist/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="/mnt/gaia/home/projects/legiolist/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>
......@@ -304,16 +304,16 @@
<post-processing>
<post-process name="create-references"/>
<post-process name="transfer-sequences"/>
<post-process name="create-chromosome-locations-and-lengths"/>
<post-process name="do-sources" />
<post-process name="populate-child-features"/>
<post-process name="create-location-range-index"/>
<post-process name="create-overlap-view" />
<post-process name="create-attribute-indexes" />
<post-process name="create-search-index" />
<post-process name="summarise-objectstore" />
<post-process name="create-autocomplete-index" />
<post-process name="transfer-sequences"/>
<post-process name="create-attribute-indexes" />
</post-processing>
</project>
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