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Merge pull request #131 from nasa/DEV_GeneLab_Reference_Annotations_v…
…GL-DPPD-7110-A GeneLab Reference Annotations Pipeline version update from GL-DPPD-7110 to GL-DPPD-7110-A
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..._Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv
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| name,species,strain,ensemblVersion,ref_source,fasta,gtf,taxon,bioconductor_annotations,custom_annotations,genelab_annots_link,genelab_annots_info_link | ||
| ARABIDOPSIS,Arabidopsis thaliana,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.59.gtf.gz,3702,org.At.tair.db,,https://figshare.com/ndownloader/files/48354355,https://figshare.com/ndownloader/files/48354352 | ||
| BACSU,Bacillus subtilis,subsp. subtilis 168,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/dna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.59.gtf.gz,224308,,org.Bsubtilissubspsubtilis168.eg.db,https://figshare.com/ndownloader/files/48354346,https://figshare.com/ndownloader/files/48354349 | ||
| BRADI,Brachypodium distachyon,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/brachypodium_distachyon/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.59.gtf.gz,15368,,org.Bdistachyon.eg.db,https://figshare.com/ndownloader/files/48354370,https://figshare.com/ndownloader/files/48354361 | ||
| BRARP,Brassica rapa,,59,ensembl_plants,http://ftp.ensemblgenomes.org/pub/plants/release-59/fasta/brassica_rapa/dna/Brassica_rapa.Brapa_1.0.dna.toplevel.fa.gz,http://ftp.ensemblgenomes.org/pub/plants/release-59/gtf/brassica_rapa/Brassica_rapa.Brapa_1.0.59.gtf.gz,,,,, | ||
| WORM,Caenorhabditis elegans,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.112.gtf.gz,6239,org.Ce.eg.db,,https://figshare.com/ndownloader/files/48354373,https://figshare.com/ndownloader/files/48354364 | ||
| ZEBRAFISH,Danio rerio,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/danio_rerio/Danio_rerio.GRCz11.112.gtf.gz,7955,org.Dr.eg.db,,https://figshare.com/ndownloader/files/48354388,https://figshare.com/ndownloader/files/48354367 | ||
| FLY,Drosophila melanogaster,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.112.gtf.gz,7227,org.Dm.eg.db,,https://figshare.com/ndownloader/files/48354382,https://figshare.com/ndownloader/files/48354376 | ||
| ERCC,,,,ThermoFisher,https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip,https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip,,,,, | ||
| ECOLI,Escherichia coli,str. K-12 substr. MG1655,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.59.gtf.gz,511145,,org.EcolistrK12substrMG1655.eg.db,https://figshare.com/ndownloader/files/48354379,https://figshare.com/ndownloader/files/48354394 | ||
| HUMAN,Homo sapiens,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz,9606,org.Hs.eg.db,,https://figshare.com/ndownloader/files/48354445,https://figshare.com/ndownloader/files/48354448 | ||
| ,Lactobacillus acidophilus,NCFM,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.gtf.gz,272621,,,https://figshare.com/ndownloader/files/49061254,https://figshare.com/ndownloader/files/49061257 | ||
| MOUSE,Mus musculus,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/mus_musculus/Mus_musculus.GRCm39.112.gtf.gz,10090,org.Mm.eg.db,,https://figshare.com/ndownloader/files/48354460,https://figshare.com/ndownloader/files/48354457 | ||
| ,Mycobacterium marinum,M,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,216594,,,https://figshare.com/ndownloader/files/49061260,https://figshare.com/ndownloader/files/49061263 | ||
| ORYSJ,Oryza sativa,Japonica,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.59.gtf.gz,39947,,,https://figshare.com/ndownloader/files/48354451,https://figshare.com/ndownloader/files/48354454 | ||
| ORYLA,Oryzias latipes,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/oryzias_latipes/Oryzias_latipes.ASM223467v1.112.gtf.gz,8090,,org.Olatipes.eg.db,https://figshare.com/ndownloader/files/48354463,https://figshare.com/ndownloader/files/48354466 | ||
| ,Pseudomonas aeruginosa,UCBPP-PA14,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.gtf.gz,208963,,,https://figshare.com/ndownloader/files/49061266,https://figshare.com/ndownloader/files/49061269 | ||
| RAT,Rattus norvegicus,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz,10116,org.Rn.eg.db,,https://figshare.com/ndownloader/files/48354472,https://figshare.com/ndownloader/files/48354475 | ||
| YEAST,Saccharomyces cerevisiae,S288C,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.112.gtf.gz,559292,org.Sc.sgd.db,,https://figshare.com/ndownloader/files/48354469,https://figshare.com/ndownloader/files/48354478 | ||
| SALTY,Salmonella enterica,serovar Typhimurium str. LT2,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.gtf.gz,99287,,org.SentericaserovarTyphimuriumstrLT2.eg.db,https://figshare.com/ndownloader/files/49061272,https://figshare.com/ndownloader/files/49061275 | ||
| ,Serratia liquefaciens,ATCC 27592,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.gtf.gz,1346614,,,https://figshare.com/ndownloader/files/49061278,https://figshare.com/ndownloader/files/49061281 | ||
| ,Staphylococcus aureus,MRSA252,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.gtf.gz,282458,,,https://figshare.com/ndownloader/files/49061284,https://figshare.com/ndownloader/files/49061287 | ||
| ,Streptococcus mutans,UA159,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.gtf.gz,210007,,,https://figshare.com/ndownloader/files/49061290,https://figshare.com/ndownloader/files/49061293 | ||
| ,Vibrio fischeri,ES114,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.gtf.gz,312309,,,https://figshare.com/ndownloader/files/49061296,https://figshare.com/ndownloader/files/49061299 |
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...ab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/CHANGELOG.md
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| # Changelog | ||
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| All notable changes to this project will be documented in this file. | ||
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| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | ||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## [1.1.0](https://github.com/nasa/GeneLab_Data_Processing/blob/DEV_GeneLab_Reference_Annotations_vGL-DPPD-7110-A/GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A) | ||
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| ### Added | ||
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| - Added software: | ||
| - AnnotationForge version 1.46.0 | ||
| - biomaRt version 2.60.1 | ||
| - GO.db version 3.19.1 | ||
| - Added support for: | ||
| - Bacillus subtilis, subsp. subtilis 168 | ||
| - Brachypodium distachyon | ||
| - Escherichia coli,str. K-12 substr. MG1655 | ||
| - Oryzias latipes | ||
| - Lactobacillus acidophilus NCFM | ||
| - Mycobacterium marinum M | ||
| - Oryza sativa Japonica | ||
| - Pseudomonas aeruginosa UCBPP-PA14 | ||
| - Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | ||
| - Serratia liquefaciens ATCC 27592 | ||
| - Staphylococcus aureus MRSA252 | ||
| - Streptococcus mutans UA159 | ||
| - Vibrio fischeri ES114 | ||
| - Added AnnotationForge helper script install-org-db.R to create | ||
| organism-specific annotation packages (org.*.eg.db) in R if not available on | ||
| Bioconductor. Used for: | ||
| - Bacillus subtilis, subsp. subtilis 168 | ||
| - Brachypodium distachyon | ||
| - Escherichia coli,str. K-12 substr. MG1655 | ||
| - Oryzias latipes | ||
| - Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | ||
| - Added NCBI as a source for FASTA and GTF files | ||
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| ### Fixed | ||
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| - Fixed processing for ECOLI | ||
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| ### Changed | ||
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| - Updated Ensembl versions: | ||
| - Animals: Ensembl release 112 | ||
| - Plants: Ensembl plants release 59 | ||
| - Bacteria: Ensembl bacteria release 59 | ||
| - Updated software: | ||
| - tidyverse version updated from 1.3.2 to 2.0.0 | ||
| - STRINGdb version updated from 2.8.4 to 2.16.4 | ||
| - PANTHER.db version updated from 1.0.11 to 1.0.12 | ||
| - rtracklayer version updated from 1.56.1 to 1.64.0 | ||
| - Bioconductor version updated from 3.15.1 to 3.19 | ||
| - Removed org.EcK12.eg.db and replaced it with a locally created annotations | ||
| database, as it is no longer available on Bioconductor | ||
| - Changed the first argument of GL-DPPD-7110-A_build-genome-annots-tab.R from | ||
| the 'name' column value to the 'species' column value (e.g., 'Mus musculus' instead of 'MOUSE') | ||
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| ## [1.0.0](https://github.com/nasa/GeneLab_Data_Processing/releases/tag/GL_RefAnnotTable_1.0.0) |
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