CHANGES IN VERSION 1.4.0 ------------------------ NEW FEATURES o add script to generate user-contributed resources o makeEnsemblGtfToGRanges() no longer stores data in S3 but downloads and converts to GRanges on the fly o add EnsemblFastaTwoBitToAHM unit test o add man page for makeEnsemblTwoBitToAHM and ensemblFastaToTwoBitFile o add makeAnnotationHubMetadata() helper MODIFICATIONS o move GSE62944-related code to ExperimentHub o move old vignettes to inst/scripts; add 'Introduction to AnnotationHubData' vignette o remove fasta and towbit files on the fly o add 'uploadToS3' argument to pushResources() and runRecipes() o move readMetadataFromCsv() from ExperimentHubData to AnnotationHubData o add 'fileName' arg to readMetadataFromCsv(); don't warn when 'Tags' are provided o specify length for args in readMetadataFromCsv() o makeAnnotationHubMetadata() populates PreparerClass with package name o add 'fileName' arg to makeAnnotationHubMetadata() CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o add makeEnsemblTwoBit() o add hubError(), hubError<- generics and methods o create 'HubMetadata' class which 'AnnotationHubMetadata' inherits from MODIFICATIONS o export ensemblFastaToTwoBitFile() o modifications due to changes in httr::HEAD(): - AFAICT httr::HEAD() >= 1.1.0 accepts https only, not ftp - use xml2 instead of XML for parsing (httr >= 1.1.0 dependency change) o work on recipes: - clean up ChEA and Gencode - don't export tracksToUpdate(); was broken and not used - reorg man pages; combine Ensembl Fasta and TwoBit on single man page o work on updateResources(): - push data to S3 before inserting metadata in db - isolate pushResources() and pushMetadata() from updateResources() - NOTE: Epigenome unit test is failing due to bad url. If not fixed by the host the recipe will need to change. o update makedbSNPVCF() to look in new clinvar location BUG FIXES o fix bugs in makedbSNPVCF() recipe related to genome and tags CHANGES IN VERSION 1.0.0 ------------------------ BUG FIXES o ENSEMBL recipes discover gtf files on Windows. CHANGES IN VERSION 0.0.214 -------------------------- NEW FEATURES o Have added vcf files from the following genome builds for humans "human_9606/VCF/clinical_vcf_set/", "human_9606_b141_GRCh37p13/VCF/", "human_9606_b142_GRCh37p13/VCF/", "human_9606_b142_GRCh37p13/VCF/clinical_vcf_set/" o For each genome build, where available, the following VCF file formats are available a) all.vcf.gz b) all_papu.vcf.gz c) common_all.vcf.gz d) clinvar.vcf.gz e) clinvar_papu f) common_and_clinical g) common_no_known_medical_impact o The user can refer to http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/ for VCF file type formats