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Adding Apis mellifera #55

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Adding Apis mellifera #55

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af80a4b
Update gxa_references.conf
anilthanki Aug 19, 2024
e169078
Update gxa_references.conf
anilthanki Aug 19, 2024
2a87e14
Update gxa_references.conf
anilthanki Aug 19, 2024
7a97827
Update genome_references.conf
anilthanki Aug 19, 2024
0b54848
Update sh/gtf/genome_references.conf
anilthanki Aug 20, 2024
feecbd2
Create apis_mellifera
anilthanki Aug 20, 2024
2d90116
Update apis_mellifera - update mysql db server
anilthanki Aug 22, 2024
c2f0402
Update validate_mysql_database_access.sh - updates user
anilthanki Aug 22, 2024
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23 changes: 23 additions & 0 deletions annsrcs/ensembl/apis_mellifera
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@@ -0,0 +1,23 @@
software.name=metazoa
software.version=51
url=http://metazoa.ensembl.org/biomart/martservice?
organism=apis mellifera
databaseName=metazoa
datasetName=amellifera_eg_gene
mySqlDbName=apis_mellifera
mySqlDbUrl=mysql-eg-publicsql.ebi.ac.uk:4157
types=ensgene,enstranscript,ensprotein
chromosomeName=CM009931.2,CM009932.2,CM009933.2,CM009934.2,CM009935.2,CM009936.2,CM009937.2,CM009938.2,CM009939.2,CM009940.2,CM009941.2,CM009942.2,CM009943.2,CM009944.2,CM009945.2,CM009946.2
property.gene_biotype=gene_biotype
property.description=description
property.ensgene=ensembl_gene_id
property.ensprotein=ensembl_peptide_id
property.enstranscript=ensembl_transcript_id
property.entrezgene=entrezgene_id
property.go=go_id
property.goterm=name_1006
property.interpro=interpro
property.interproterm=interpro_description
property.refseq=refseq_peptide
property.symbol=external_gene_name
property.uniprot=uniprotsptrembl,uniprotswissprot
1 change: 1 addition & 0 deletions sh/gtf/genome_references.conf
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Expand Up @@ -262,6 +262,7 @@ zea_mays 4577 plants ftp://ftp.ebi.ac.uk/ensemblgenomes/pub/DOTrelease-RELNO/pla
plasmodium_berghei 5821 protists ftp://ftp.ensemblgenomes.org/pub/DOTrelease-RELNO/protists/fasta/plasmodium_berghei/dna/Plasmodium_berghei.PBANKA01.dna.toplevel.fa.gz ftp://ftp.ensemblgenomes.org/pub/DOTrelease-RELNO/protists/fasta/plasmodium_berghei/cdna/Plasmodium_berghei.PBANKA01.cdna.all.fa.gz ftp://ftp.ensemblgenomes.org/pub/DOTrelease-RELNO/protists/gtf/plasmodium_berghei/Plasmodium_berghei.PBANKA01.RELNO.gtf.gz PBANKA01
salmo_salar 8030 ensembl /nfs/ftp/ensemblftp/ensembl/PRIVATE/release-RELNO/fasta/salmo_salar/dna/Salmo_salar.Ssal_v3.1.dna.toplevel.fa.gz /nfs/ftp/ensemblftp/ensembl/PRIVATE/release-RELNO/fasta/salmo_salar/cdna/Salmo_salar.Ssal_v3.1.cdna.all.fa.gz /nfs/ftp/ensemblftp/ensembl/PRIVATE/release-RELNO/gtf/salmo_salar/Salmo_salar.Ssal_v3.1.RELNO.gtf.gz Ssal_v3.1
anopheles_gambiae 7165 metazoa ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/fasta/anopheles_gambiae/dna/Anopheles_gambiae.AgamP4.dna.toplevel.fa.gz ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/fasta/anopheles_gambiae/cdna/Anopheles_gambiae.AgamP4.cdna.all.fa.gz ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/gtf/anopheles_gambiae/Anopheles_gambiae.AgamP4.RELNO.gtf.gz AgamP4
apis_mellifera 7460 metazoa ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/fasta/apis_mellifera/dna/Apis_mellifera.Amel_HAv3.1.dna.toplevel.fa.gz ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/fasta/apis_mellifera/cdna/Apis_mellifera.Amel_HAv3.1.cdna.all.fa.gz ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/gtf/apis_mellifera/Apis_mellifera.Amel_HAv3.1.RELNO.gtf.gz Amel_HAv3.1
# Manually added
ciona_savignyi 51511 ensembl /nfs/ftp/ensemblftp/ensembl/PRIVATE/release-RELNO/fasta/ciona_savignyi/dna/Ciona_savignyi.CSAV2.0.dna.toplevel.fa.gz /nfs/ftp/ensemblftp/ensembl/PRIVATE/release-RELNO/fasta/ciona_savignyi/cds/Ciona_savignyi.CSAV2.0.cds.all.fa.gz /nfs/ftp/ensemblftp/ensembl/PRIVATE/release-RELNO/gtf/ciona_savignyi/Ciona_savignyi.CSAV2.0.RELNO.gtf.gz CSAV2.0
dictyostelium_discoideum 352472 protists http://ftp.ensemblgenomes.org/pub/protists/release-RELNO/fasta/dictyostelium_discoideum/dna/Dictyostelium_discoideum.dicty_2.7.dna.toplevel.fa.gz http://ftp.ensemblgenomes.org/pub/protists/release-RELNO/fasta/dictyostelium_discoideum/cdna/Dictyostelium_discoideum.dicty_2.7.cdna.all.fa.gz http://ftp.ensemblgenomes.org/pub/protists/release-RELNO/gtf/dictyostelium_discoideum/Dictyostelium_discoideum.dicty_2.7.RELNO.gtf.gz dicty_2.7
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1 change: 1 addition & 0 deletions sh/gtf/gxa_references.conf
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Expand Up @@ -3,6 +3,7 @@ amborella_trichopoda ftp://ftp.ensemblgenomes.org/pub/plants/release-RELNO/gtf/a
anas_platyrhynchos ftp://ftp.ensembl.org/pub/release-RELNO/gtf/anas_platyrhynchos_platyrhynchos/Anas_platyrhynchos_platyrhynchos.CAU_duck1.0.RELNO.gtf.gz
anolis_carolinensis ftp://ftp.ensembl.org/pub/release-RELNO/gtf/anolis_carolinensis/Anolis_carolinensis.AnoCar2.0v2.RELNO.gtf.gz
anopheles_gambiae ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/gtf/anopheles_gambiae/Anopheles_gambiae.AgamP4.RELNO.gtf.gz
apis_mellifera ftp://ftp.ensemblgenomes.org/pub/metazoa/release-RELNO/gtf/apis_mellifera/Apis_mellifera.Amel_HAv3.1.RELNO.gtf.gz
arabidopsis_lyrata ftp://ftp.ensemblgenomes.org/pub/release-RELNO/plants/gtf/arabidopsis_lyrata/Arabidopsis_lyrata.v.1.0.RELNO.gtf.gz
arabidopsis_thaliana ftp://ftp.ensemblgenomes.org/pub/release-RELNO/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.RELNO.gtf.gz
aspergillus_fumigatus ftp://ftp.ensemblgenomes.org/pub/fungi/release-RELNO/gtf/aspergillus_fumigatus/Aspergillus_fumigatus.ASM265v1.RELNO.gtf.gz
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2 changes: 1 addition & 1 deletion sh/validate_mysql_database_access.sh
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Expand Up @@ -8,7 +8,7 @@ SOFTWARE_VERSION=$(grep 'software.version' $config_file | awk -F'=' '{ print $2
MYSQL_DB_NAME=$(grep 'mySqlDbName' $config_file | awk -F'=' '{ print $2 }')"_core_"$SOFTWARE_VERSION

if [[ $type =~ ensembl ]]; then
MYSQL_USER=ensro
MYSQL_USER=anonymous
elif [[ $type =~ wbps ]]; then
MYSQL_USER=ensro
else
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