f86cc1e3f913432f81ad47733aae8e78ab9500c6 markd Mon May 27 12:06:58 2019 -0700 output total number of aligned bases in pslStats -overallStats diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk index 04a93e0..159f4bc 100644 --- src/hg/makeDb/outside/gencode/gencodeLoad.mk +++ src/hg/makeDb/outside/gencode/gencodeLoad.mk @@ -24,69 +24,57 @@ export SHELLOPTS=pipefail ## # programs, etc ## mach = $(shell uname -m) ## # Release info and files from Sanger. # BEGIN EDIT THESE EACH RELEASE # # - ensemblPrevVersion is use to get chrom name mappings for pre-release, # as this doesn't change between release. ## #db = hg38 -#db = hg19 -db = mm10 -#db = grcHhh38 +db = hg19 +#db = mm10 #preRelease = no preRelease = yes ifeq (${db},mm10) grcRefAssembly = GRCm38 ver = M22 prevVer = M21 gencodeOrg = Gencode_mouse ftpReleaseSubdir = release_${ver} annGffTypeName = chr_patch_hapl_scaff.annotation ensemblVer = 97_38 ensemblPrevVer = 96_38 ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer} else ifeq (${db},hg38) grcRefAssembly = GRCh38 ver = 31 prevVer = 30 gencodeOrg = Gencode_human ftpReleaseSubdir = release_${ver} annGffTypeName = chr_patch_hapl_scaff.annotation ensemblVer = 97_38 ensemblPrevVer = 96_38 ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer} -else ifeq (${db},grcHhh38) - # hg38 with patches - grcRefAssembly = GRCh38 - ver = 28 - prevVer = 27 - gencodeOrg = Gencode_human - ftpReleaseSubdir = release_${ver} - annGffTypeName = chr_patch_hapl_scaff.annotation - ensemblVer = 94_38 - ensemblPrevVer = 93_38 - ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer} else ifeq (${db},hg19) grcRefAssembly = GRCh37 - verBase = 30 + verBase = 31 ver = ${verBase}lift37 ftpReleaseSubdir = release_${verBase}/GRCh37_mapping prevVer = 29lift37 gencodeOrg = Gencode_human annGffTypeName = annotation ensemblVer = 74_37 # only used to get genome chromsome name mappings ensemblPrevVer = ${ensemblVer} # doesn't change ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer} isBackmap = yes else $(error unimplement genome database: ${db}) endif # END EDIT THESE EACH RELEASE