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Commit 2868d811 authored by Remi PLANEL's avatar Remi PLANEL
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Update source location

parent baf42fe6
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Showing with 71 additions and 28 deletions
project.xml
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......@@ -11,17 +11,40 @@
<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/legiolist/genomes/gff/legiolist-gff/LegioParis"/>
<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 name="LegioParis-chromosome-fasta" type="fasta">
<property name="fasta.taxonId" value="297246"/>
<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/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/>
</source>
<source name="LegioParis-ncbi-gff" type="legiolist-gff">
<source name="LegioParis-protein-gene" type="legiolist-gene-prot">
<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.includes" value="LegioParis_10-05-2012_LegioList-prot-gene.tsv"/>
</source>
<source name="LegioParis-protein-fasta" type="fasta">
<property name="fasta.taxonId" value="297246"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
<property name="fasta.classAttribute" value="primaryIdentifier"/>
<property name="fasta.sequenceType" value="protein" />
<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>
<!-- <source name="LegioParis-ncbi-gff" type="legiolist-gff">
<property name="gff3.taxonId" value="297246"/>
<property name="gff3.seqDataSourceName" value="NCBI LegioParis"/>
<property name="gff3.dataSourceName" value="NCBI"/>
......@@ -38,7 +61,7 @@
<property name="fasta.includes" value="GCF_000048645.1_ASM4864v1_genomic.fna"/>
</source>
-->
<source name="Lfallonii-gff" type="legiolist-gff">
......@@ -47,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lfallonii"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lfallonii"/>
</source>
<source name="Lfallonii-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -55,10 +78,29 @@
<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/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lfallonii-protein-gene" type="legiolist-gene-prot">
<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.includes" value="Lfallonii-prot-gene.tsv"/>
</source>
<source name="Lfallonii-protein-fasta" type="fasta">
<property name="fasta.taxonId" value="96230"/>
<property name="fasta.dataSetTitle" value="Legiolist Lfallonii protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
<property name="fasta.classAttribute" value="primaryIdentifier"/>
<property name="fasta.sequenceType" value="protein" />
<property name="fasta.sequenceType" value="protein" />
<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"/>
</source>
<source name="Lhackeliae-gff" type="legiolist-gff">
<property name="gff3.taxonId" value="449"/>
......@@ -66,7 +108,7 @@
<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/legiolist/genomes/gff/legiolist-gff/Lhackeliae"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lhackeliae"/>
</source>
<source name="Lhackeliae-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -74,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -85,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lmicadei"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lmicadei"/>
</source>
<source name="Lmicadei-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -93,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -104,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Long_Mage"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Long_Mage"/>
</source>
<source name="Long_Mage-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -112,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -124,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lorraine"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/Lorraine"/>
</source>
<source name="lorraine-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -132,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -145,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpAlcoy"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpAlcoy"/>
</source>
<source name="LpAlcoy-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -153,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -165,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpCorby"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpCorby"/>
</source>
<source name="LpCorby-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -173,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -187,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpLens"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpLens"/>
</source>
<source name="LpLens-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -195,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
......@@ -206,7 +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="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpPhila"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/gff/clean/LpPhila"/>
</source>
<source name="LpPhila-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
......@@ -214,10 +256,10 @@
<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/legiolist/genomes/fasta/legiolist"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/genome/fasta"/>
</source>
<source name="uniprot" type="uniprot">
<!-- <source name="uniprot" type="uniprot">
<property name="uniprot.organisms" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/uniprot"/>
<property name="creatego" value="true"/>
......@@ -225,12 +267,11 @@
<property name="allowduplicates" value="false"/>
<property name="loadfragments" value="true"/>
<property name="loadtrembl" value="true"/>
</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" location="/mnt/gaia/home/projects/legiolist/data/pre-process-data/"/>
<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>
......@@ -244,12 +285,12 @@
</source>
<source name="go" type="go">
<property name="src.data.file" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/go/go-basic.obo"/>
<property name="src.data.file" location="/mnt/gaia/home/projects/legiolist/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/legiolist/genomes/publication"/>
<property name="src.data.dir" location="/mnt/gaia/home/projects/legiolist/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>
......@@ -267,6 +308,8 @@
<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" />
......
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