From 455a94530110ba2323f68f6de4408a499e3449b2 Mon Sep 17 00:00:00 2001 From: Stephen Newhouse Date: Tue, 8 Sep 2015 15:03:19 +0100 Subject: [PATCH] dev updates Tue 8 Sep 2015 15:03:19 BST --- Makefile | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 64 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index d6df4ad..5185ea5 100755 --- a/Makefile +++ b/Makefile @@ -291,6 +291,69 @@ hg19: wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hg19/ucsc.hg19.stidx && \ chmod -R 775 $(INSTALLDIR)/ngs_projects/ngseasy_resources/reference_genomes_hg19/ +## hs37d5 +hs37d5: + @echo "Get hs37d5 Genomes indexed and resources" + cd $(INSTALLDIR)/ngs_projects/ngseasy_resources && \ + mkdir -p reference_genomes_hs37d5 && \ + cd $(INSTALLDIR)/ngs_projects/ngseasy_resources/reference_genomes_hs37d5 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/1000G_omni2.5.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/1000G_omni2.5.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/1000G_phase1.indels.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/1000G_phase1.indels.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/1000G_phase1.snps.high_confidence.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/1000G_phase1.snps.high_confidence.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/CEUTrio.HiSeq.WGS.b37.NA12878.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/CEUTrio.HiSeq.WGS.b37.NA12878.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/contaminant_list.fa && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/dbsnp_138.b37.excluding_sites_after_129.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/dbsnp_138.b37.excluding_sites_after_129.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/dbsnp_138.b37.recab && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/dbsnp_138.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/dbsnp_138.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/Genome && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/GenomeIndex && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/GenomeIndexHash && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hapmap_3.3.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hapmap_3.3.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.1.bt2 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.2.bt2 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.3.bt2 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.4.bt2 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.amb && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.ann && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.bwt && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.fai && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.novoindex && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.pac && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.fasta.sa && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.rev.1.bt2 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.rev.2.bt2 && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.sthash && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/hs37d5.stidx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/human_g1k_v37_0.5Kwindows.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/human_g1k_v37_1Kwindows.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/LCR_hg19_rmsk.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/Mills_and_1000G_gold_standard.indels.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/Mills_and_1000G_gold_standard.indels.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/NA12878.knowledgebase.snapshot.20131119.b37.vcf && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/NA12878.knowledgebase.snapshot.20131119.b37.vcf.idx && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/nexterarapidcapture_exome_targetedregions_v1.2.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/nexterarapidcapture_expandedexome_targetedregions.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/OverflowTable && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/S03723314_Regions.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/S06588914_Regions_trimmed.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/SeqCap_EZ_Exome_v3_capture.bed && \ + wget https://s3-eu-west-1.amazonaws.com/ngseasy.data/reference_genomes_hs37d5/SeqCap_EZ_Exome_v3_primary.bed && \ + chmod -R 775 $(INSTALLDIR)/ngs_projects/ngseasy_resources/reference_genomes_hs37d5/ + ## Test data and stick it in raw_fastq @@ -337,7 +400,7 @@ annovardb: --rm=true \ -i -t compbio/ngseasy-annovar:$(VERSION) \ /bin/bash -c \ - "/bin/bash /usr/local/pipeline/annovar/get_annovar_gene_databases.sh && /bin/bash /usr/local/pipeline/annovar/get_annovar_databases.sh" + "/bin/bash /usr/local/pipeline/annovar/get_annovar_gene_databases.sh && \bin/bash /usr/local/pipeline/annovar/get_annovar_databases.sh" ## Cleanups clean: