Skip to content

Commit db3162e

Browse files
matthdsmmatthdsm
committed
GGD recipes, FTP > HTTP where available
1 parent 37f4218 commit db3162e

32 files changed

+45
-45
lines changed

‎ggd-recipes/GRCh37/clinvar.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ recipe:
1111
recipe_cmds:
1212
- |
1313
release=20170905
14-
baseurl=ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2017/clinvar_${release}.vcf.gz
14+
baseurl=http://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2017/clinvar_${release}.vcf.gz
1515
mkdir -p variation
1616
wget -c -O variation/clinvar-orig.vcf.gz $baseurl
1717
[[ -f variation/clinvar.vcf.gz ]] || zcat variation/clinvar-orig.vcf.gz | bgzip -c > variation/clinvar.vcf.gz

‎ggd-recipes/GRCh37/dbsnp.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ recipe:
1111
version=150
1212
org=human_9606_b${version}_GRCh37p13
1313
release=20170710
14-
url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/GATK/All_${release}.vcf.gz
14+
url=http://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/GATK/All_${release}.vcf.gz
1515
mkdir -p variation
1616
wget -c -O variation/dbsnp-$version-orig.vcf.gz $url
1717
[[ -f variation/dbsnp-$version.vcf.gz ]] || zcat variation/dbsnp-$version-orig.vcf.gz | sed "s/^chrM/MT/g" | sed "s/^chr//g" | bgzip -c > variation/dbsnp-$version.vcf.gz

‎ggd-recipes/GRCh37/giab-NA12878-NA24385-somatic.yaml

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Truth set for NA12878/NA24385 somatic mixture
2-
# ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
2+
# http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
33
---
44
attributes:
55
name: giab-NA12878-NA24385-somatic
@@ -10,7 +10,7 @@ recipe:
1010
recipe_cmds:
1111
- |
1212
dir=validation/giab-NA12878-NA24385-somatic
13-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
13+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
1414
calls=na12878-na24385-somatic-truth.vcf.gz
1515
regions=na12878-na24385-somatic-truth-regions.bed
1616
mkdir -p $dir

‎ggd-recipes/GRCh37/giab-NA12878.yaml

+4-4
Original file line numberDiff line numberDiff line change
@@ -9,15 +9,15 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA12878
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/
1313
calls=HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz
1414
regions=HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed
1515
mkdir -p $dir
1616
wget -c -O $dir/truth_small_variants.vcf.gz $url/$calls
1717
tabix -f -p vcf $dir/truth_small_variants.vcf.gz
18-
wget -c -O $dir/truth_regions.bed $url/$regions
19-
wget -O - ftp://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Personalis_1000_Genomes_deduplicated_deletions.bed | grep -v ^Chr > $dir/truth_DEL.bed
20-
wget -O - ftp://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Spiral_Genetics_insertions.bed | grep -v ^Chr > $dir/truth_INS.bed
18+
wget -c -O $dir/truth_regions.bed $url/$regions
19+
wget -O - http://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Personalis_1000_Genomes_deduplicated_deletions.bed | grep -v ^Chr > $dir/truth_DEL.bed
20+
wget -O - http://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Spiral_Genetics_insertions.bed | grep -v ^Chr > $dir/truth_INS.bed
2121
recipe_outfiles:
2222
- validation/giab-NA12878/truth_small_variants.vcf.gz
2323
- validation/giab-NA12878/truth_small_variants.vcf.gz.tbi

‎ggd-recipes/GRCh37/giab-NA24385.yaml

+3-3
Original file line numberDiff line numberDiff line change
@@ -11,20 +11,20 @@ recipe:
1111
recipe_cmds:
1212
- |
1313
dir=validation/giab-NA24385
14-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/
14+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/
1515
calls=HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
1616
regions=HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
1717
mkdir -p $dir
1818
wget -c -O $dir/truth_small_variants.vcf.gz $url/$calls
1919
tabix -f -p vcf $dir/truth_small_variants.vcf.gz
20-
wget -c -O $dir/truth_regions.bed $url/$regions
20+
wget -c -O $dir/truth_regions.bed $url/$regions
2121
delurl=https://s3.amazonaws.com/bcbio/giab/NA24385/NA24385-GIAB-2tech-dels-v0_1_8-GRCh37.bed.gz
2222
wget -c -O $dir/truth_DEL_giab.bed.gz $delurl
2323
wget -c -O $dir/truth_DEL_giab.bed.gz.tbi $delurl.tbi
2424
cnvurl=https://s3.amazonaws.com/bcbio/giab/NA24385/NA24385-crowd-dels-GRCh37.bed.gz
2525
wget -c -O $dir/truth_DEL_crowd.bed.gz $cnvurl
2626
wget -c -O $dir/truth_DEL_crowd.bed.gz.tbi $cnvurl.tbi
27-
svurl=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/svanalyzer_union_171212_v0.5.0_annotated.vcf.gz
27+
svurl=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/svanalyzer_union_171212_v0.5.0_annotated.vcf.gz
2828
wget -c -O $dir/truth_sv.vcf.gz $svurl
2929
wget -c -O $dir/truth_sv.vcf.gz.tbi $svurl.tbi
3030
recipe_outfiles:

‎ggd-recipes/GRCh37/giab-NA24631.yaml

+2-2
Original file line numberDiff line numberDiff line change
@@ -9,13 +9,13 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA24631
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/
1313
calls=HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf.vcf.gz
1414
regions=HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf_noMetaSV.bed
1515
mkdir -p $dir
1616
wget -c -O $dir/truth_small_variants.vcf.gz $url/$calls
1717
tabix -f -p vcf $dir/truth_small_variants.vcf.gz
18-
wget -c -O $dir/truth_regions.bed $url/$regions
18+
wget -c -O $dir/truth_regions.bed $url/$regions
1919
recipe_outfiles:
2020
- validation/giab-NA24631/truth_small_variants.vcf.gz
2121
- validation/giab-NA24631/truth_small_variants.vcf.gz.tbi

‎ggd-recipes/GRCh37/gnomad.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ recipe:
88
recipe_type: bash
99
recipe_cmds:
1010
- |
11-
url=ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz
11+
url=http://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz
1212
ref=../seq/GRCh37.fa
1313
mkdir -p variation
1414
export TMPDIR=`pwd`

‎ggd-recipes/GRCz11/seq.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ recipe:
88
recipe_cmds:
99
- |
1010
BUILD=GRCz11
11-
url=ftp://ftp.ensembl.org/pub/release-92/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.toplevel.fa.gz
11+
url=http://ftp.ensembl.org/pub/release-92/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.toplevel.fa.gz
1212
mkdir -p seq
1313
wget --no-check-certificate -O - $url | gunzip -c > seq/$BUILD.fa
1414
samtools faidx seq/$BUILD.fa

‎ggd-recipes/Sscrofa11.1/seq.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ recipe:
88
recipe_cmds:
99
- |
1010
BUILD=Sscrofa11.1
11-
url=ftp://ftp.ensembl.org/pub/release-92/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna_rm.toplevel.fa.gz
11+
url=http://ftp.ensembl.org/pub/release-92/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna_rm.toplevel.fa.gz
1212
mkdir -p seq
1313
wget --no-check-certificate -O - $url | gunzip -c > seq/$BUILD.fa
1414
samtools faidx seq/$BUILD.fa

‎ggd-recipes/hg19/clinvar.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ recipe:
1111
recipe_cmds:
1212
- |
1313
release=20170905
14-
baseurl=ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2017/clinvar_${release}.vcf.gz
14+
baseurl=http://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2017/clinvar_${release}.vcf.gz
1515
mkdir -p variation
1616
wget -c -O variation/clinvar-orig.vcf.gz $baseurl
1717
[[ -f variation/clinvar.vcf.gz ]] || zcat variation/clinvar-orig.vcf.gz | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" | bgzip -c > variation/clinvar.vcf.gz

‎ggd-recipes/hg19/dbsnp.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ recipe:
1111
version=150
1212
org=human_9606_b${version}_GRCh37p13
1313
release=20170710
14-
url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/GATK/All_${release}.vcf.gz
14+
url=http://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/GATK/All_${release}.vcf.gz
1515
mkdir -p variation
1616
wget -c -O variation/dbsnp-$version-orig.vcf.gz $url
1717
[[ -f variation/dbsnp-$version.vcf.gz ]] || zcat variation/dbsnp-$version-orig.vcf.gz | bgzip -c > variation/dbsnp-$version.vcf.gz

‎ggd-recipes/hg19/giab-NA12878.yaml

+3-3
Original file line numberDiff line numberDiff line change
@@ -12,16 +12,16 @@ recipe:
1212
- |
1313
dir=validation/giab-NA12878
1414
remapurl=https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh37_ensembl2UCSC.txt
15-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/
15+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/
1616
calls=HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz
1717
regions=HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed
1818
mkdir -p $dir
1919
wget -qO- $remapurl | awk '{if($1!=$2) print "s/^"$1"/"$2"/g"}' > remap.sed
2020
wget -c -O - $url/$calls | gunzip -c | sed -f remap.sed | grep -v "##contig=" | bgzip -c > $dir/truth_small_variants.vcf.gz
2121
tabix -f -p vcf $dir/truth_small_variants.vcf.gz
2222
wget -c -O - $url/$regions | sed -f remap.sed > $dir/truth_regions.bed
23-
wget -O - ftp://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Personalis_1000_Genomes_deduplicated_deletions.bed | grep -v ^Chr | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" > $dir/truth_DEL.bed
24-
wget -O - ftp://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Spiral_Genetics_insertions.bed | grep -v ^Chr | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" > $dir/truth_INS.bed
23+
wget -O - http://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Personalis_1000_Genomes_deduplicated_deletions.bed | grep -v ^Chr | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" > $dir/truth_DEL.bed
24+
wget -O - http://ftp.ncbi.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Spiral_Genetics_insertions.bed | grep -v ^Chr | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" > $dir/truth_INS.bed
2525
recipe_outfiles:
2626
- validation/giab-NA12878/truth_small_variants.vcf.gz
2727
- validation/giab-NA12878/truth_small_variants.vcf.gz.tbi

‎ggd-recipes/hg19/giab-NA24385.yaml

+2-2
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA24385
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/
1313
calls=HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
1414
regions=HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
1515
remapurl=https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh37_ensembl2UCSC.txt
@@ -24,7 +24,7 @@ recipe:
2424
cnvurl=https://s3.amazonaws.com/bcbio/giab/NA24385/NA24385-crowd-dels-hg19.bed.gz
2525
wget -c -O $dir/truth_DEL_crowd.bed.gz $cnvurl
2626
wget -c -O $dir/truth_DEL_crowd.bed.gz.tbi $cnvurl.tbi
27-
svurl=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/svanalyzer_union_171212_v0.5.0_annotated.vcf.gz
27+
svurl=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/svanalyzer_union_171212_v0.5.0_annotated.vcf.gz
2828
wget -c -O - $svurl | gunzip -c | sed -f remap.sed | grep -v "##contig=" | bgzip -c > $dir/truth_sv.vcf.gz
2929
tabix -f -p vcf $dir/truth_sv.vcf.gz
3030
recipe_outfiles:

‎ggd-recipes/hg19/giab-NA24631.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA24631
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/
1313
calls=HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf.vcf.gz
1414
regions=HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf_noMetaSV.bed
1515
remapurl=https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh37_ensembl2UCSC.txt

‎ggd-recipes/hg19/gnomad.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ recipe:
99
recipe_type: bash
1010
recipe_cmds:
1111
- |
12-
url=ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz
12+
url=http://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz
1313
remap_url=https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh37_ensembl2UCSC.txt
1414
ref=../seq/hg19.fa
1515
mkdir -p variation

‎ggd-recipes/hg38-noalt/README.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
Human reference genome: GRCh38/hg38 without any alternative reference contigs
22

3-
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/
3+
http://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

‎ggd-recipes/hg38-noalt/bowtie2.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ recipe:
1010
- |
1111
base=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index
1212
new=hg38-noalt.fa
13-
ncbiurl=ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids
13+
ncbiurl=http://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids
1414
wget -c $ncbiurl/$base.tar.gz
1515
[[ -f $base.1.bt2 ]] || tar -xzvpf $base.tar.gz
1616
mkdir -p bowtie2

‎ggd-recipes/hg38-noalt/bwa.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ recipe:
1010
- |
1111
base=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
1212
new=hg38-noalt.fa
13-
ncbiurl=ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids
13+
ncbiurl=http://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids
1414
wget -c $ncbiurl/$base.bwa_index.tar.gz
1515
[[ -f $base.fna.bwt ]] || tar -xzvpf $base.bwa_index.tar.gz
1616
mkdir -p bwa

‎ggd-recipes/hg38-noalt/gtf.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ recipe:
1010
recipe_type: bash
1111
recipe_cmds:
1212
- |
13-
url=ftp://ftp.ensembl.org/pub/release-78/gtf/homo_sapiens/Homo_sapiens.GRCh38.78.gtf.gz
13+
url=http://ftp.ensembl.org/pub/release-78/gtf/homo_sapiens/Homo_sapiens.GRCh38.78.gtf.gz
1414
mkdir -p rnaseq
1515
remap_url=http://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_ensembl2UCSC.txt
1616
wget -qO- $remap_url | awk '{if($1!=$2) print "s/^"$1"/"$2"/g"}' > remap.sed

‎ggd-recipes/hg38/README.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
Full hg38/GRCh38 reference genome distributed by 1000 genomes
22
Derived from NCBI set with HLA and decoy alternative alleles
3-
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
3+
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/

‎ggd-recipes/hg38/bwa.yaml

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
# Full hg38/GRCh38 reference genome distributed by 1000 genomes
22
# Derived from NCBI set with HLA and decoy alternative alleles
3-
# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
3+
# http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
44
# Pre-build bwa indices
55
---
66
attributes:
@@ -11,7 +11,7 @@ recipe:
1111
recipe_type: bash
1212
recipe_cmds:
1313
- |
14-
url=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome
14+
url=http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome
1515
base=GRCh38_full_analysis_set_plus_decoy_hla.fa
1616
new=hg38.fa
1717
mkdir -p bwa

‎ggd-recipes/hg38/clinvar.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ recipe:
1111
recipe_cmds:
1212
- |
1313
release=20170905
14-
baseurl=ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2017/clinvar_${release}.vcf.gz
14+
baseurl=http://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2017/clinvar_${release}.vcf.gz
1515
mkdir -p variation
1616
wget -c -O variation/clinvar-orig.vcf.gz $baseurl
1717
[[ -f variation/clinvar.vcf.gz ]] || zcat variation/clinvar-orig.vcf.gz | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" | bgzip -c > variation/clinvar.vcf.gz

‎ggd-recipes/hg38/dbsnp.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ recipe:
1313
version=150
1414
org=human_9606_b${version}_GRCh38p7
1515
release=20170710
16-
url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/GATK/All_${release}.vcf.gz
16+
url=http://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/GATK/All_${release}.vcf.gz
1717
mkdir -p variation
1818
wget -c -O variation/dbsnp-$version-orig.vcf.gz $url
1919
[[ -f variation/dbsnp-$version.vcf.gz ]] || zcat variation/dbsnp-$version-orig.vcf.gz | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" | bgzip -c > variation/dbsnp-$version.vcf.gz

‎ggd-recipes/hg38/giab-NA12878-NA24385-somatic.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Truth set for NA12878/NA24385 somatic mixture
2-
# ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
2+
# http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
33
---
44
attributes:
55
name: giab-NA12878-NA24385-somatic

‎ggd-recipes/hg38/giab-NA12878.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA12878
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh38/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh38/
1313
calls=HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz
1414
regions=HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed
1515
mkdir -p $dir

‎ggd-recipes/hg38/giab-NA24385.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA24385
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/
1313
calls=HG002_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
1414
regions=HG002_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
1515
mkdir -p $dir

‎ggd-recipes/hg38/giab-NA24631.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ recipe:
99
recipe_cmds:
1010
- |
1111
dir=validation/giab-NA24631
12-
url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/
12+
url=http://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/
1313
calls=HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.vcf.gz
1414
regions=HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.bed
1515
mkdir -p $dir

0 commit comments

Comments
 (0)