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genolist
legiolist
Commits
2868d811
Commit
2868d811
authored
Mar 05, 2020
by
Remi PLANEL
Browse files
Update source location
parent
baf42fe6
Changes
1
Hide whitespace changes
Inline
Side-by-side
project.xml
View file @
2868d811
...
...
@@ -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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/Lfallonii"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/gff/le
giolist-gff
/Lhackeliae"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/Lmicadei"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/Long_Mage"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/Lorraine"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/LpAlcoy"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/LpCorby"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/LpLens"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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
/genome
s
/gff/le
giolist-gff
/LpPhila"
/>
<property
name=
"src.data.dir"
location=
"/
mnt/gaia/home
/projects/legiolist
/data/pre-process-data
/genome/gff/
c
le
an
/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
/genome
s
/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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