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master.yaml
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spur31:
metadata:
name: spur31
common_name: purple sea urchin
custom: false
description: corresponds to GCA_000002235.2
downloader: joselynn
ncbi_taxon_id: 7668
ensembl_release_number: 43
accession:
genbank: null
refseq: null
organism: Strongylocentrotus purpuratus
organization: ensembl metazoa
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-09-03 15:48:48.715120'
commands:
- wget ftp://ftp.ensemblgenomes.org/pub/metazoa/release-43/fasta/strongylocentrotus_purpuratus/dna/CHECKSUMS
- wget ftp://ftp.ensemblgenomes.org/pub/metazoa/release-43/fasta/strongylocentrotus_purpuratus/dna/Strongylocentrotus_purpuratus.Spur_3.1.dna.toplevel.fa.gz
- md5sum * > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/spur31/primary
files:
- CHECKSUMS
- metadata.txt
- final_checksums.md5
uuid: cc303697-34ce-3cd1-b883-5d709a4f3e09
annotations:
- component: gtf
complete:
status: true
time: '2019-09-18 14:52:56.723157'
commands:
- wget ftp://ftp.ensemblgenomes.org/pub/metazoa/release-43/gtf/strongylocentrotus_purpuratus/CHECKSUMS
- wget ftp://ftp.ensemblgenomes.org/pub/metazoa/release-43/gtf/strongylocentrotus_purpuratus/Strongylocentrotus_purpuratus.Spur_3.1.43.gtf.gz
- gunzip -c Strongylocentrotus_purpuratus.Spur_3.1.43.gtf.gz > Strongylocentrotus_purpuratus.Spur_3.1.43.gtf
- md5sum * > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/spur31/gtf
files:
- Strongylocentrotus_purpuratus.Spur_3.1.43.gtf
- Strongylocentrotus_purpuratus.Spur_3.1.43.gtf.gz
- CHECKSUMS
- metadata.txt
- final_checksums.md5
uuid: 6983397c-e268-31e2-bd0d-db7d47c589f9
cdubliniensis_cd36:
metadata:
name: cdubliniensis_cd36
common_name: yeast
ncbi_taxon_id: 573826
organism: Candida dubliniensis CD36
organization: http://www.candidagenome.org
custom: false
description: C. dubliniensis CD36 was sequenced by the Wellcome Trust Sanger Institute
(Jackson et al., 2009, Genome Res. 19:2231-2244). Sequence and annotation obtained
by CGD from EBI.
downloader: joselynn wallace
ensembl_release_number: null
accession:
genbank: null
refseq: null
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-09-04 17:08:11.656257'
commands:
- wget http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/current/C_dubliniensis_CD36_current_chromosomes.fasta.gz
- md5sum * > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/cdubliniensis_cd36/primary
files:
- C_dubliniensis_CD36_current_chromosomes.fasta.gz
- C_dubliniensis_CD36_current_chromosomes.fasta.gz.1
- metadata.txt
- final_checksums.md5
uuid: 3889615c-c609-377c-a49a-2376d7bb4ee1
broad_bundle_hg19:
metadata:
name: broad_bundle_hg19
common_name: human
custom: false
description: see https://software.broadinstitute.org/gatk/download/bundle
downloader: fgelin
ncbi_taxon_id: 9606
ensembl_release_number: null
accession:
genbank: null
refseq: null
organism: Homo sapiens
organization: broad institute
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-09-05 09:24:59.920666'
commands:
- wget --user='gsapubftp-anonymous' 'ftp://ftp.broadinstitute.org/bundle/hg19/*.fasta.gz*'
- wget --user='gsapubftp-anonymous' 'ftp://ftp.broadinstitute.org/bundle/hg19/*.vcf.*'
- ls -a1 .*.done | xargs rm
- md5sum *.gz > postdownload-checksums.md5
- gunzip *.gz
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/broad_bundle_hg19/primary
files:
- CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.idx.gz.md5
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.gz.md5
- dbsnp_138.hg19.vcf.idx.gz.md5
- 1000G_omni2.5.hg19.sites.vcf.idx.gz.md5
- dbsnp_138.hg19.excluding_sites_after_129.vcf
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.idx.gz.md5
- ucsc.hg19.dict
- CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf
- 1000G_phase1.indels.hg19.sites.vcf.idx.gz.md5
- dbsnp_138.hg19.excluding_sites_after_129.vcf.idx.gz.md5
- ucsc.hg19.fasta.fai.gz.md5
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.idx
- postdownload-checksums.md5
- 1000G_omni2.5.hg19.sites.vcf.gz.md5
- 1000G_phase1.indels.hg19.sites.vcf
- 1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx.gz.md5
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.idx
- NA12878.knowledgebase.snapshot.20131119.hg19.vcf.idx.gz.md5
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.gz.md5
- hapmap_3.3.hg19.sites.vcf.gz.md5
- 1000G_phase1.indels.hg19.sites.vcf.gz.md5
- 1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx
- hapmap_3.3.hg19.sites.vcf.idx.gz.md5
- Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
- Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx.gz.md5
- CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.gz.md5
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.idx.gz.md5
- hapmap_3.3_hg19_pop_stratified_af.vcf.gz.tbi
- 1000G_omni2.5.hg19.sites.vcf.idx
- 1000G_phase1.snps.high_confidence.hg19.sites.vcf
- 1000G_omni2.5.hg19.sites.vcf
- Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx
- dbsnp_138.hg19.vcf.gz.md5
- NA12878.knowledgebase.snapshot.20131119.hg19.vcf
- ucsc.hg19.fasta.gz.md5
- hapmap_3.3.hg19.sites.vcf.idx
- provinence.txt
- NA12878.knowledgebase.snapshot.20131119.hg19.vcf.idx
- ucsc.hg19.fasta
- Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz.md5
- hapmap_3.3.hg19.sites.vcf
- dbsnp_138.hg19.vcf.idx
- metadata.txt
- hapmap_3.3_hg19_pop_stratified_af.vcf
- 1000G_phase1.indels.hg19.sites.vcf.idx
- dbsnp_138.hg19.vcf
- CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.idx
- final_checksums.md5
- dbsnp_138.hg19.excluding_sites_after_129.vcf.idx
- NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf
- dbsnp_138.hg19.excluding_sites_after_129.vcf.gz.md5
- final-checksums.md5
- ucsc.hg19.fasta.fai
- 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz.md5
- ucsc.hg19.dict.gz.md5
- NA12878.knowledgebase.snapshot.20131119.hg19.vcf.gz.md5
uuid: b2588931-2b94-3d8b-9eab-c8fa153af515
drosophila-melanogaster-bdgp6rel9:
metadata:
name: drosophila-melanogaster-bdgp6rel9
common_name: fly
custom: false
description: The genome assembly represented here corresponds to GenBank Assembly
ID GCA_000001215.4
downloader: fgelin
ncbi_taxon_id: 7227
ensembl_release_number: 91
accession:
genbank: null
refseq: null
organism: Drosophila melanogaster
organization: ensembl
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-09-05 16:23:22.609416'
commands:
- wget ftp://ftp.ensembl.org/pub/release-91/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz
- wget ftp://ftp.ensembl.org/pub/release-91/fasta/drosophila_melanogaster/dna/CHECKSUMS
- grep "dna.toplevel" CHECKSUMS > checksum.ensembl
- gunzip -c Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz > Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- sum Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz
- md5sum Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz > checksum.md5
- md5sum Drosophila_melanogaster.BDGP6.dna.toplevel.fa >> checksum.md5
- mkdir Drosophila_melanogaster.BDGP6.rel91
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/primary
files:
- checksum.ensembl
- checksum.md5
- Drosophila_melanogaster.BDGP6.rel91
- CHECKSUMS
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- metadata.txt
- final_checksums.md5
uuid: f00c482a-8550-31b9-89fb-803d4f9edbb5
annotations:
- component: gtf
complete:
status: true
time: '2019-09-18 15:04:10.854805'
commands:
- wget ftp://ftp.ensembl.org/pub/release-91/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.91.gtf.gz
- wget ftp://ftp.ensembl.org/pub/release-91/gtf/drosophila_melanogaster/CHECKSUMS
- gunzip -c Drosophila_melanogaster.BDGP6.91.gtf.gz > Drosophila_melanogaster.BDGP6.91.gtf
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/gtf
files:
- Drosophila_melanogaster.BDGP6.91.gtf.gz
- Drosophila_melanogaster.BDGP6.91.gtf
- CHECKSUMS
- metadata.txt
- final_checksums.md5
uuid: e3e260a5-87ff-36a1-8526-c73a9b03ec44
indices:
- component: bwa_index_0_7_17
complete:
status: true
time: '2019-09-27 10:40:18.828504'
src: f00c482a-8550-31b9-89fb-803d4f9edbb5
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/primary/Drosophila_melanogaster.BDGP6.dna.toplevel.fa
/gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bwa_index_0_7_17/Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- cd /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bwa_index_0_7_17
- bwa index Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bwa_index_0_7_17
files:
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.ann
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.pac
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.sa
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.amb
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.bwt
- metadata.txt
- final_checksums.md5
uuid: 6206259e-fe61-35a2-9773-6a491c17aa11
- component: bowtie2_index_2_3_0
complete:
status: true
time: '2019-10-29 16:24:40.073570'
src: f00c482a-8550-31b9-89fb-803d4f9edbb5
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/primary/Drosophila_melanogaster.BDGP6.dna.toplevel.fa
/gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bowtie2_index_2_3_0/Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- cd /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bowtie2_index_2_3_0
- bowtie2-build Drosophila_melanogaster.BDGP6.dna.toplevel.fa drosophila-melanogaster-bdgp6rel9
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bowtie2_index_2_3_0
files:
- drosophila-melanogaster-bdgp6rel9.4.bt2
- drosophila-melanogaster-bdgp6rel9.2.bt2
- drosophila-melanogaster-bdgp6rel9.3.bt2
- drosophila-melanogaster-bdgp6rel9.rev.2.bt2
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- drosophila-melanogaster-bdgp6rel9.1.bt2
- drosophila-melanogaster-bdgp6rel9.rev.1.bt2
- metadata.txt
- final_checksums.md5
uuid: 6206259e-fe61-35a2-9773-6a491c17aa11
- component: bedtools_genome_file
complete:
status: true
time: '2020-01-31 08:41:47.494750'
src: f00c482a-8550-31b9-89fb-803d4f9edbb5
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/primary/Drosophila_melanogaster.BDGP6.dna.toplevel.fa
/gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bedtools_genome_file/Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- cd /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bedtools_genome_file
- samtools faidx Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- awk -v OFS='\t' {'print $1,$2'} Drosophila_melanogaster.BDGP6.dna.toplevel.fa.fai
> Drosophila_melanogaster.BDGP6.dna.toplevel.genomeFile.txt
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/drosophila-melanogaster-bdgp6rel9/bedtools_genome_file
files:
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa.fai
- Drosophila_melanogaster.BDGP6.dna.toplevel.genomeFile.txt
- Drosophila_melanogaster.BDGP6.dna.toplevel.fa
- metadata.txt
- final_checksums.md5
uuid: 6206259e-fe61-35a2-9773-6a491c17aa11
wbps8_ws256:
metadata:
name: wbps8_ws256
common_name: worm
organism: Caenorhabditis elegans
organization: wormbase_parasite
custom: false
downloader: fgelin
description: none
ncbi_taxon_id: 6239
ensembl_release_number: null
accession:
genbank: null
refseq: null
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-09-17 14:37:07.472786'
commands:
- wget ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS8/species/caenorhabditis_elegans/PRJNA13758/caenorhabditis_elegans.PRJNA13758.WBPS8.genomic.fa.gz
- gunzip -c caenorhabditis_elegans.PRJNA13758.WBPS8.genomic.fa.gz > caenorhabditis_elegans.PRJNA13758.WBPS8.genomic.fa
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/wbps8_ws256/primary
files:
- caenorhabditis_elegans.PRJNA13758.WBPS8.canonical_geneset.gtf.gz.1
- caenorhabditis_elegans.PRJNA13758.WBPS8.canonical_geneset.gtf.gz
- caenorhabditis_elegans.PRJNA13758.WBPS8.genomic.fa.gz.1
- caenorhabditis_elegans.PRJNA13758.WBPS8.genomic.fa
- caenorhabditis_elegans.PRJNA13758.WBPS8.genomic.fa.gz
- caenorhabditis_elegans.PRJNA13758.WBPS8.canonical_geneset.gtf
uuid: 27010656-d97a-11e9-9007-40f2e9026890
- component: cdna-trandscriptome
complete:
status: true
time: '2019-09-17 14:37:07.515180'
commands:
- wget ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS8/species/caenorhabditis_elegans/PRJNA13758/caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa.gz
- gunzip -c caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa.gz >
caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa
- cat caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa | awk '{if($1
~ ">" ) {split($1,a,".");$1=a[1]}; print }' > caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon.fa
- cat caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa | awk '{if($1
~ ">" ) {split($1,a,".");$1=a[1]; split($2,b,"."); $2=b[1];} print }' > caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon2.fa
- cat caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa | awk '{if($1
~ ">" ) {split($2,b,"."); $2=b[1];} print }' > caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon3.fa
- mkdir salmon_index_0_11_2
- salmon index -t caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa
-i salmon_index_0_11_2/c_elegans_PRJNA13758_WBPS8_mRNA_orig_index --type
quasi -k 25
- salmon index -t caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon2.fa
-i salmon_index_0_11_2/c_elegans_PRJNA13758_WBPS8_mRNA_transcripts_index --type
quasi -k 25
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/wbps8_ws256/cdna-trandscriptome
files:
- caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon.fa
- caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon3.fa
- caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa.gz.1
- salmon_index_0_11_2_test
- provinence.txt
- caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa.gz
- caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.fa
- caenorhabditis_elegans.PRJNA13758.WBPS8.mRNA_transcripts.salmon2.fa
- metadata.txt
uuid: 2701712c-d97a-11e9-9007-40f2e9026890
annotations:
- component: gtf
commands:
- wget ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS8/species/caenorhabditis_elegans/PRJNA13758/caenorhabditis_elegans.PRJNA13758.WBPS8.canonical_geneset.gtf.gz
- gunzip -c caenorhabditis_elegans.PRJNA13758.WBPS8.canonical_geneset.gtf.gz
> caenorhabditis_elegans.PRJNA13758.WBPS8.canonical_geneset.gtf
- md5sum *.* > final_checksums.md5
grch37_release87:
metadata:
name: grch37_release87
common_name: human
organism: Homo sapiens
organization: ensembl
downloader: fgelin
description: corresponds to GenBank Assembly ID GCA_000001405.14
ncbi_taxon_id: 9606
ensembl_release_number: 87
custom: false
accession:
genbank: null
refseq: null
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-09-18 10:01:26.314885'
commands:
- wget ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary
files:
- provinence.txt
- Homo_sapiens.GRCh37.87.gtf.gz
- metadata.txt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
uuid: ce1b1916-da1c-11e9-bf4d-40f2e9026674
- component: primary
complete:
status: true
time: '2020-02-13 14:31:22.998592'
commands:
- gunzip -c Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz > Homo_sapiens.GRCh37.dna.primary_assembly.fa
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary
files:
- bwa_index_0_7_17
- bowtie2_index_2_3_0
- provinence.txt
- Homo_sapiens.GRCh37.87.gtf.gz
- metadata.txt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
uuid: 6afd026e-4e97-11ea-8dd6-40f2e9026674
annotations:
- component: gtf
complete:
status: true
time: '2019-09-18 15:11:40.419184'
commands:
- wget ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
- wget ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/CHECKSUMS
- gunzip -c Homo_sapiens.GRCh37.87.gtf.gz > Homo_sapiens.GRCh37.87.gtf
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/gtf
files:
- CHECKSUMS
- Homo_sapiens.GRCh37.87.gtf.gz
- metadata.txt
- final_checksums.md5
- Homo_sapiens.GRCh37.87.gtf
uuid: 7c0adc0d-a657-3919-8b77-9bb294b7823c
indices:
- component: bowtie2_index_2_3_0
complete:
status: true
time: '2019-11-11 11:26:29.370497'
src: ce1b1916-da1c-11e9-bf4d-40f2e9026674
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
/gpfs/data/shared/databases/refchef_refs/grch37_release87/bowtie2_index_2_3_0/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
- cd /gpfs/data/shared/databases/refchef_refs/grch37_release87/bowtie2_index_2_3_0
- gunzip -c Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz > Homo_sapiens.GRCh37.dna.primary_assembly.fa
- bowtie2-build Homo_sapiens.GRCh37.dna.primary_assembly.fa grch37_rel87
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/bowtie2_index_2_3_0
files:
- grch37_rel87.3.bt2
- grch37_rel87.rev.1.bt2
- grch37_rel87.4.bt2
- grch37_rel87.2.bt2
- grch37_rel87.1.bt2
- metadata.txt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
- final_checksums.md5
- grch37_rel87.rev.2.bt2
uuid: 24b510d3-0a73-3211-98da-274317c2a032
- component: bwa_index_0_7_17
complete:
status: true
time: '2019-11-11 12:42:06.679344'
src: ce1b1916-da1c-11e9-bf4d-40f2e9026674
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
/gpfs/data/shared/databases/refchef_refs/grch37_release87/bwa_index_0_7_17/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
- cd /gpfs/data/shared/databases/refchef_refs/grch37_release87/bwa_index_0_7_17
- gunzip -c Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz > Homo_sapiens.GRCh37.dna.primary_assembly.fa
- bwa index Homo_sapiens.GRCh37.dna.primary_assembly.fa
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/bwa_index_0_7_17
files:
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.ann
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.sa
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.bwt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.amb
- metadata.txt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
- final_checksums.md5
- Homo_sapiens.GRCh37.dna.primary_assembly.fa.pac
uuid: 2161bca8-8c03-3b52-958a-a232158e2c71
- component: gmapdb_2017-01-14
complete:
status: true
time: '2020-02-13 14:37:35.306595'
src: ce1b1916-da1c-11e9-bf4d-40f2e9026674
commands:
- source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
- /gpfs/runtime/cbc_conda/cbc_conda_v1_root/envs/bioflows/bin/gmap_make_ref.sh
Ensembl_Homo_sapiens_GRCh37 /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary/Homo_sapiens.GRCh37.dna.primary_assembly.fa
/gpfs/data/shared/databases/refchef_refs/grch37_release87/gtf/Homo_sapiens.GRCh37.87.gtf
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/gmapdb_2017-01-14
files:
- Ensembl_Homo_sapiens_GRCh37.maps
- Ensembl_Homo_sapiens_GRCh37.ref153offsets64meta
- Ensembl_Homo_sapiens_GRCh37.genomecomp
- Ensembl_Homo_sapiens_GRCh37.sachildexc
- Ensembl_Homo_sapiens_GRCh37.saindex64strm
- Ensembl_Homo_sapiens_GRCh37.ref153offsets64strm
- Ensembl_Homo_sapiens_GRCh37.chrsubset
- Ensembl_Homo_sapiens.GRCh37.87.introns
- Ensembl_Homo_sapiens_GRCh37.ref153positions
- Ensembl_Homo_sapiens.GRCh37.dna.primary_assembly.fa
- Ensembl_Homo_sapiens_GRCh37.version
- Ensembl_Homo_sapiens_GRCh37.chromosome
- Ensembl_Homo_sapiens_GRCh37.salcpchilddc
- Ensembl_Homo_sapiens_GRCh37.contig
- Ensembl_Homo_sapiens_GRCh37.sarray
- Ensembl_Homo_sapiens_GRCh37.saindex64meta
- Ensembl_Homo_sapiens_GRCh37.sachildguide1024
- Ensembl_Homo_sapiens_GRCh37.chromosome.iit
- Ensembl_Homo_sapiens_GRCh37.contig.iit
- Ensembl_Homo_sapiens.GRCh37.87.gtf
- Ensembl_Homo_sapiens.GRCh37.87.splicesites
- metadata.txt
- Ensembl_Homo_sapiens_GRCh37.salcpexc
- Ensembl_Homo_sapiens_GRCh37.genomebits128
- Ensembl_Homo_sapiens_GRCh37.salcpguide1024
uuid: 48e57f7a-4e98-11ea-b3b2-40f2e9026674
- component: hisat2_index_2_2_1
complete:
status: true
time: '2020-12-09 11:11:23.356131'
src: 6afd026e-4e97-11ea-8dd6-40f2e9026674
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary/Homo_sapiens.GRCh37.dna.primary_assembly.fa
/gpfs/data/shared/databases/refchef_refs/grch37_release87/hisat2_index_2_2_1/Homo_sapiens.GRCh37.dna.primary_assembly.fa
- cd /gpfs/data/shared/databases/refchef_refs/grch37_release87/hisat2_index_2_2_1
- hisat2-build Homo_sapiens.GRCh37.dna.primary_assembly.fa Homo_sapiens.GRCh37
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/hisat2_index_2_2_1
files:
- Homo_sapiens.GRCh37.7.ht2
- Homo_sapiens.GRCh37.6.ht2
- Homo_sapiens.GRCh37.8.ht2
- Homo_sapiens.GRCh37.4.ht2
- Homo_sapiens.GRCh37.1.ht2
- Homo_sapiens.GRCh37.2.ht2
- Homo_sapiens.GRCh37.3.ht2
- metadata.txt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa
- final_checksums.md5
- Homo_sapiens.GRCh37.5.ht2
uuid: 1c86abd8-bd0a-3071-a1ab-9b5ff6a5cb36
- component: star_index_2_7_6a
complete:
status: true
time: '2020-12-09 11:50:28.930872'
src: 6afd026e-4e97-11ea-8dd6-40f2e9026674
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grch37_release87/primary/Homo_sapiens.GRCh37.dna.primary_assembly.fa
/gpfs/data/shared/databases/refchef_refs/grch37_release87/star_index_2_7_6a/Homo_sapiens.GRCh37.dna.primary_assembly.fa
- cd /gpfs/data/shared/databases/refchef_refs/grch37_release87/star_index_2_7_6a
- STAR --runMode genomeGenerate --genomeDir /gpfs/data/shared/databases/refchef_refs/grch37_release87/star_index_2_7_6a
--genomeFastaFiles /gpfs/data/shared/databases/refchef_refs/grch37_release87/star_index_2_7_6a/Homo_sapiens.GRCh37.dna.primary_assembly.fa
--sjdbGTFfile /gpfs/data/shared/databases/refchef_refs/grch37_release87/gtf/Homo_sapiens.GRCh37.87.gtf
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grch37_release87/star_index_2_7_6a
files:
- chrName.txt
- exonInfo.tab
- SAindex
- Genome
- geneInfo.tab
- sjdbList.out.tab
- sjdbInfo.txt
- transcriptInfo.tab
- sjdbList.fromGTF.out.tab
- chrLength.txt
- genomeParameters.txt
- chrStart.txt
- SA
- chrNameLength.txt
- metadata.txt
- Homo_sapiens.GRCh37.dna.primary_assembly.fa
- final_checksums.md5
- exonGeTrInfo.tab
uuid: 5c67d3d5-9fa7-39a6-9410-310ac1cc4385
grcm38_p5:
metadata:
name: grcm38_p5
common_name: mouse
organization: ensembl
downloader: aleith
organism: Mus musculus
description: corresponds to GenBank Assembly ID GCA_000001635.7
ncbi_taxon_id: 10090
custom: false
ensembl_release_number: 89
accession:
genbank: null
refseq: null
category: genomics
levels:
references:
- component: primary
complete:
status: true
time: '2019-11-05 15:25:00.993081'
commands:
- wget ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
- md5sum *.* > post_download.md5
- gunzip -c Mus_musculus.GRCm38.dna.primary_assembly.fa.gz > Mus_musculus.GRCm38.dna.primary_assembly.fa
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/primary
files:
- Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
- post_download.md5
- Mus_musculus.GRCm38.dna.primary_assembly.fa
- metadata.txt
- final_checksums.md5
uuid: beed20fa-f897-35bf-808d-0c1ee6173274
- component: cdna-transcriptome
complete:
status: true
time: '2019-11-05 15:43:47.999012'
commands:
- wget ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
- md5sum *.* > post_download.md5
- gunzip -c Mus_musculus.GRCm38.cdna.all.fa.gz > Mus_musculus.GRCm38.cdna.all.fa
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/cdna-transcriptome
files:
- post_download.md5
- Mus_musculus.GRCm38.cdna.all.fa
- metadata.txt
- Mus_musculus.GRCm38.cdna.all.fa.gz
- final_checksums.md5
uuid: 54a37969-f245-3a78-aec3-d2c6034bbd27
annotations:
- component: gtf
complete:
status: true
time: '2019-11-05 15:48:04.689398'
commands:
- wget ftp://ftp.ensembl.org/pub/release-89/gtf/mus_musculus/Mus_musculus.GRCm38.89.gtf.gz
- wget ftp://ftp.ensembl.org/pub/release-89/gtf/mus_musculus/CHECKSUMS
- gunzip -c Mus_musculus.GRCm38.89.gtf.gz > Mus_musculus.GRCm38.89.gtf
- md5sum *.* > final_chechsums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/gtf
files:
- CHECKSUMS
- metadata.txt
- Mus_musculus.GRCm38.89.gtf
- Mus_musculus.GRCm38.89.gtf.gz
- final_chechsums.md5
uuid: 907f4f2a-000d-11ea-9a67-40f2e9026674
- component: gff3
complete:
status: true
time: '2020-07-24 17:25:47.905424'
commands:
- wget ftp://ftp.ensembl.org/pub/release-89/gff3/mus_musculus/Mus_musculus.GRCm38.89.gff3.gz
- wget ftp://ftp.ensembl.org/pub/release-89/gff3/mus_musculus/CHECKSUMS
- gunzip -c Mus_musculus.GRCm38.89.gff3.gz > Mus_musculus.GRCm38.89.gff3
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/gff3
files:
- Mus_musculus.GRCm38.89.gff3
- CHECKSUMS
- Mus_musculus.GRCm38.89.gff3.gz
- metadata.txt
- final_checksums.md5
uuid: b04a1dd9-a779-3e2e-afba-e8c928bc6a9a
indices:
- component: salmon_index_0_11_2
complete:
status: true
time: '2019-12-04 10:51:30.768189'
src: 54a37969-f245-3a78-aec3-d2c6034bbd27
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/cdna-transcriptome/Mus_musculus.GRCm38.cdna.all.fa
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all.fa
- cd /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($1,a,".");$1=a[1]};
print }' > Mus_musculus.GRCm38.cdna.all.salmon.fa
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($1,a,".");$1=a[1];
split($4,b,"."); $4=b[1];} print }' > Mus_musculus.GRCm38.cdna.all.salmon2.fa
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($4,b,".");
$4=b[1];} print }' > Mus_musculus.GRCm38.cdna.all.salmon3.fa
- salmon index -t Mus_musculus.GRCm38.cdna.all.fa -i Mus_musculus.GRCm38.cdna.all_orig_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i Mus_musculus.GRCm38.cdna.all_transcripts_index
--type quasi -k 31
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_fmd_index
--type fmd
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon2.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_sal_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon3.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_sal3_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_index
--type quasi -k 31
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2
files:
- salmon_index_0_11_2
- Mus_musculus.GRCm38.cdna.all_transcripts_index
- Mus_musculus.GRCm38.cdna.all.salmon.fa
- Mus_musculus.GRCm38.cdna.all_orig_index
- Mus_musculus.GRCm38.cdna.all.fa
- Mus_musculus.GRCm38.cdna.all.salmon2.fa
- metadata.txt
- Mus_musculus.GRCm38.cdna.all.salmon3.fa
- final_checksums.md5
uuid: 482c6e70-389e-3559-8c19-d86cac067060
- component: salmon_index_0_11_2
complete:
status: true
time: '2019-12-04 11:02:53.817264'
src: 54a37969-f245-3a78-aec3-d2c6034bbd27
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/cdna-transcriptome/Mus_musculus.GRCm38.cdna.all.fa
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all.fa
- cd /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($1,a,".");$1=a[1]};
print }' > Mus_musculus.GRCm38.cdna.all.salmon.fa
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($1,a,".");$1=a[1];
split($4,b,"."); $4=b[1];} print }' > Mus_musculus.GRCm38.cdna.all.salmon2.fa
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($4,b,".");
$4=b[1];} print }' > Mus_musculus.GRCm38.cdna.all.salmon3.fa
- salmon index -t Mus_musculus.GRCm38.cdna.all.fa -i Mus_musculus.GRCm38.cdna.all_orig_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i Mus_musculus.GRCm38.cdna.all_transcripts_index
--type quasi -k 31
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_fmd_index
--type fmd
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon2.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_sal_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon3.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_sal3_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_index
--type quasi -k 31
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2
files:
- salmon_index_0_11_2
- Mus_musculus.GRCm38.cdna.all_transcripts_index
- Mus_musculus.GRCm38.cdna.all.salmon.fa
- Mus_musculus.GRCm38.cdna.all_orig_index
- Mus_musculus.GRCm38.cdna.all.fa
- Mus_musculus.GRCm38.cdna.all.salmon2.fa
- metadata.txt
- Mus_musculus.GRCm38.cdna.all.salmon3.fa
- final_checksums.md5
uuid: 482c6e70-389e-3559-8c19-d86cac067060
- component: salmon_index_0_11_2
complete:
status: true
time: '2019-12-04 11:14:18.997289'
src: 54a37969-f245-3a78-aec3-d2c6034bbd27
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/cdna-transcriptome/Mus_musculus.GRCm38.cdna.all.fa
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all.fa
- cd /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($1,a,".");$1=a[1]};
print }' > Mus_musculus.GRCm38.cdna.all.salmon.fa
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($1,a,".");$1=a[1];
split($4,b,"."); $4=b[1];} print }' > Mus_musculus.GRCm38.cdna.all.salmon2.fa
- cat Mus_musculus.GRCm38.cdna.all.fa | awk '{if($1 ~ ">" ) {split($4,b,".");
$4=b[1];} print }' > Mus_musculus.GRCm38.cdna.all.salmon3.fa
- salmon index -t Mus_musculus.GRCm38.cdna.all.fa -i Mus_musculus.GRCm38.cdna.all_orig_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i Mus_musculus.GRCm38.cdna.all_transcripts_index
--type quasi -k 31
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_fmd_index
--type fmd
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon2.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_sal_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon3.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_sal3_index
--type quasi -k 25
- salmon index -t Mus_musculus.GRCm38.cdna.all.salmon.fa -i salmon_index_0_11_2/Mus_musculus.GRCm38.cdna.all_transcripts_index
--type quasi -k 31
- mkdir /gpfs/data/shared/databases/refchef_refs/grcm38_p5/cdna-transcriptome/salmon_index_0_11_2
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2/*.*
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/cdna-transcriptome/salmon_index_0_11_2/
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/salmon_index_0_11_2
files:
- salmon_index_0_11_2
- Mus_musculus.GRCm38.cdna.all_transcripts_index
- Mus_musculus.GRCm38.cdna.all.salmon.fa
- Mus_musculus.GRCm38.cdna.all_orig_index
- Mus_musculus.GRCm38.cdna.all.fa
- Mus_musculus.GRCm38.cdna.all.salmon2.fa
- metadata.txt
- Mus_musculus.GRCm38.cdna.all.salmon3.fa
- final_checksums.md5
uuid: 482c6e70-389e-3559-8c19-d86cac067060
- component: bwa_index_0_7_17
src: beed20fa-f897-35bf-808d-0c1ee6173274
complete:
status: true
time: '2020-01-31 13:14:58.874052'
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/primary/Mus_musculus.GRCm38.dna.primary_assembly.fa
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/bwa_index_0_7_17/Mus_musculus.GRCm38.dna.primary_assembly.fa
- cd /gpfs/data/shared/databases/refchef_refs/grcm38_p5/bwa_index_0_7_17
- bwa index us_musculus.GRCm38.dna.primary_assembly.fa
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/bwa_index_0_7_17
files:
- Mus_musculus.GRCm38.dna.primary_assembly.fa.ann
- Mus_musculus.GRCm38.dna.primary_assembly.fa.pac
- Mus_musculus.GRCm38.dna.primary_assembly.fa.bwt
- Mus_musculus.GRCm38.dna.primary_assembly.fa.amb
- Mus_musculus.GRCm38.dna.primary_assembly.fa
- metadata.txt
- Mus_musculus.GRCm38.dna.primary_assembly.fa.sa
- final_checksums.md5
uuid: 482c6e70-389e-3559-8c19-d86cac067060
- component: bowtie2_index_2_3_0
src: beed20fa-f897-35bf-808d-0c1ee6173274
complete:
status: true
time: '2020-01-31 13:22:15.174774'
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/primary/Mus_musculus.GRCm38.dna.primary_assembly.fa
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/bowtie2_index_2_3_0/Mus_musculus.GRCm38.dna.primary_assembly.fa
- cd /gpfs/data/shared/databases/refchef_refs/grcm38_p5/bowtie2_index_2_3_0
- bowtie2-build Mus_musculus.GRCm38.dna.primary_assembly.fa grcm38_p5
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/bowtie2_index_2_3_0
files:
- grcm38_p5.rev.2.bt2
- grcm38_p5.4.bt2
- Mus_musculus.GRCm38.dna.primary_assembly.fa
- grcm38_p5.2.bt2
- grcm38_p5.rev.1.bt2
- metadata.txt
- grcm38_p5.1.bt2
- final_checksums.md5
- grcm38_p5.3.bt2
uuid: 482c6e70-389e-3559-8c19-d86cac067060
- component: bismark_index_0_22_3
src: beed20fa-f897-35bf-808d-0c1ee6173274
complete:
status: true
time: '2020-01-31 13:26:05.791519'
commands:
- ln -s /gpfs/data/shared/databases/refchef_refs/grcm38_p5/primary/Mus_musculus.GRCm38.dna.primary_assembly.fa
/gpfs/data/shared/databases/refchef_refs/grcm38_p5/bismark_index_0_22_3/Mus_musculus.GRCm38.dna.primary_assembly.fa
- cd /gpfs/data/shared/databases/refchef_refs/grcm38_p5/bismark_index_0_22_3
- bismark_genome_preparation .
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/grcm38_p5/bismark_index_0_22_3
files:
- metadata.txt
uuid: 24c6e462-4457-11ea-8845-40f2e9026674
nt_db:
metadata:
name: nt_db
common_name: nucleotide blast db
ncbi_taxon_id: na
organism: na
organization: ncbi
custom: false
description: Partially non-redundant nucleotide sequences from all traditional
divisions of GenBank, EMBL, and DDBJ excluding GSS,STS, PAT, EST, HTG, and WGS
downloader: joselynn wallace
ensembl_release_number: none
accession:
genbank: null
refseq: null
category: genomics
levels:
references:
- component: blast_db
complete:
status: true
time: '2019-09-20 14:56:20.030519'
commands:
- rsync --append-verify rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.gz .
- rsync --append-verify rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.gz.md5 .
- ls *.gz |xargs -n1 tar -xzf
- md5sum *.* > final_checksums.md5
location: /gpfs/data/shared/databases/refchef_refs/nt_db/blast_db
files:
- nt.69.nsi
- nt.64.nhr
- nt.75.nhd
- nt.57.nhd
- nt.26.nsq
- nt.20.nni
- nt.29.nhi
- nt.12.nsq
- nt.72.nsd
- nt.59.nin
- nt.47.tar.gz.md5
- nt.32.nhr
- nt.51.nni
- nt.19.nsi
- nt.41.nhi
- nt.00.nnd
- nt.60.nin
- nt.21.nhd
- nt.29.nhd
- nt.11.nhr
- nt.57.tar.gz.md5
- nt.31.nsd
- nt.63.nhi
- nt.27.nsq
- nt.09.nsd
- nt.27.nog
- nt.66.nin
- nt.54.tar.gz.md5
- nt.39.nin
- nt.17.nog
- nt.56.nnd
- nt.16.tar.gz
- nt.63.tar.gz.md5
- nt.32.nnd
- nt.60.nsq
- nt.79.tar.gz
- nt.80.tar.gz.md5
- nt.80.nsd
- nt.45.nhr
- nt.54.nsi
- nt.06.nin
- nt.55.nhi
- nt.07.tar.gz.md5
- nt.13.nni
- nt.71.nhr
- nt.15.tar.gz
- nt.10.nsq
- nt.19.nsq
- nt.17.tar.gz.md5
- nt.34.nsq
- nt.73.tar.gz
- nt.08.nhr
- nt.22.nhd
- nt.23.nin
- nt.17.nhr
- nt.70.nsi
- nt.47.nsq
- nt.01.nhi
- nt.35.tar.gz.md5
- nt.40.nsi
- nt.80.nsi
- nt.54.nni
- nt.65.nnd
- nt.77.nhd
- nt.48.nin
- nt.37.tar.gz.md5
- nt.51.nsd
- nt.72.nhi
- nt.55.nog
- nt.22.nsi
- nt.37.nsd
- nt.43.nnd
- nt.67.nsq
- nt.04.nin
- nt.60.nhd
- nt.32.tar.gz
- nt.54.nhr
- nt.00.tar.gz.md5
- nt.08.nnd
- nt.41.nhd
- nt.57.tar.gz
- nt.66.nhi
- nt.70.tar.gz.md5
- nt.38.nhd
- nt.65.nsi
- nt.27.nhr
- nt.39.tar.gz.md5
- nt.43.nni
- nt.58.tar.gz
- nt.25.nsq
- nt.30.nhd
- nt.11.nog
- nt.14.nsq
- nt.13.nog
- nt.35.nsd
- nt.04.nnd
- nt.58.nnd
- nt.05.nsq
- nt.45.tar.gz.md5
- nt.54.nin
- nt.63.nsq
- nt.67.nin
- nt.62.tar.gz.md5
- nt.77.nhr
- nt.16.nnd
- nt.23.tar.gz
- nt.25.nog
- nt.07.nni
- nt.31.nog
- nt.29.nni
- nt.18.tar.gz
- nt.51.nog
- nt.45.nnd
- nt.47.nhd
- nt.80.nog
- nt.48.nhr