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Using HTTP protocol instead of FTP everywhere (#451).
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@holtgrewe
holtgrewe committed May 21, 2019
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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# Jannovar Changelog

## v0.31 (UNRELEASED)

### jannovar-cli

- Using HTTP protocol instead of FTP everywhere as it's possible (#451).

## v0.30

Bugfix release.
Expand Down
124 changes: 62 additions & 62 deletions jannovar-cli/src/main/resources/default_sources.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz
Expand All @@ -68,34 +68,34 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownTo
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gtf=ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/release-54/fasta/homo_sapiens/cdna/Homo_sapiens.NCBI36.54.cdna.all.fa.gz
gtf=http://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
cdna=http://ftp.ensembl.org/pub/release-54/fasta/homo_sapiens/cdna/Homo_sapiens.NCBI36.54.cdna.all.fa.gz

; HG18 from RefSeq
[hg18/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz

; HG18 from RefSeq (only curated data sets)
[hg18/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz

; ---------------------------------------------------------------------------
; hg19/GRCh37
Expand All @@ -106,7 +106,7 @@ rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.g
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format=chr_accessions
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
Expand All @@ -119,55 +119,55 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownTo
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format=chr_accessions
gtf=ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz
table_gene_main=ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz.bz2
table_hgnc=ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz.bz2
table_entrezgene=ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz.bz2
gtf=http://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
cdna=http://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz
table_gene_main=http://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz.bz2
table_hgnc=http://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz.bz2
table_entrezgene=http://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz.bz2

; HG19 from RefSeq
[hg19/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz

; HG19 from RefSeq (only curated data sets)
[hg19/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz

; HG19 from RefSeq interim alignment (see https://www.ncbi.nlm.nih.gov/books/NBK430989/#_news_02-14-2017-interim-annotation-update-human_)
[hg19/refseq_interim]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz

; HG19 from RefSeq interim alignment, only curated (see https://www.ncbi.nlm.nih.gov/books/NBK430989/#_news_02-14-2017-interim-annotation-update-human_)
[hg19/refseq_interim_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz

; ---------------------------------------------------------------------------
; hg38/GRCh38
Expand All @@ -178,7 +178,7 @@ rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/i
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions.format=chr_accessions
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownGene.txt.gz
Expand All @@ -191,34 +191,34 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownTo
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions.format=chr_accessions
gtf=ftp://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
table_gene_main=ftp://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz
table_hgnc=ftp://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz
table_entrezgene=ftp://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz
gtf=http://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz
cdna=http://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
table_gene_main=http://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz
table_hgnc=http://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz
table_entrezgene=http://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz

; HG38 from RefSeq
[hg38/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz

; HG38 from RefSeq (only curated data sets)
[hg38/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz

; ---------------------------------------------------------------------------
; mm9
Expand All @@ -229,7 +229,7 @@ rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions.format=chr_accessions
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/knownGene.txt.gz
Expand All @@ -242,31 +242,31 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/knownToL
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions.format=chr_accessions
gtf=ftp://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/cdna/Mus_musculus.NCBIM37.67.cdna.all.fa.gz
gtf=http://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz
cdna=http://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/cdna/Mus_musculus.NCBIM37.67.cdna.all.fa.gz

; MM9 from RefSeq
[mm9/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz

; MM9 from RefSeq (only curated data sets)
[mm9/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz

; ---------------------------------------------------------------------------
; mm10
Expand All @@ -277,7 +277,7 @@ rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions.format=chr_accessions
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz
Expand All @@ -290,31 +290,31 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownTo
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions.format=chr_accessions
gtf=ftp://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/Mus_musculus.GRCm38.74.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/release-74/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.74.cdna.all.fa.gz
gtf=http://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/Mus_musculus.GRCm38.74.gtf.gz
cdna=http://ftp.ensembl.org/pub/release-74/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.74.cdna.all.fa.gz

; MM10 from RefSeq
[mm10/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz

; MM10 from RefSeq (only curated data sets)
[mm10/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4
chrToAccessions.format=chr_accessions
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz
gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz
rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz

; ---------------------------------------------------------------------------
; rn6
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