CHANGES IN VERSION 1.29.0
------------------------
NEW FEATURES
o 1.29.2 Added HIC as acceptable source type
o 1.29.1 Added CDF as acceptable source type
CHANGES IN VERSION 1.25.0
------------------------
SIGNIFICANT UPDATES
o 1.25.7 Update recipes to upload to azure. NonStandardOrgDb release recipe
updated
o 1.25.6 Update recipes to upload to azure. TwoBit ensembl and release
recipes for standard TxDb and OrgDb updated
NEW FEATURES
o 1.25.5 Add helper function to upload to azure
MODIFICATIONS
o 1.25.2 Changed makeAnnotationHubMetadata to point to Azure instead of AWS
CHANGES IN VERSION 1.21.0
------------------------
MODIFICATIONS
o 1.21.9 Add PNG as valid source type
o 1.21.4 Removed vignette for creating annotation hub package. Reference and
refer to single vignette in AnnotationHub
o 1.21.3 Tags for database now combination of biocViews and meta$Tags. Also
checks for valid AnnotationHub or AnnotationHubSoftware biocViews.
o 1.21.2 Add mtx.gz as valid source type
BUG CORRECTION
o 1.21.3 Fixed bug to run make*HubMetadata using "."
INTERNAL BUG CORRECTION
o 1.21.1 misplaced ! clause
REMOVED
o 1.21.5 Removed BioPax. url no longer valid. Resources were old and never
used beyond first addition
CHANGES IN VERSION 1.19.0
------------------------
INTERNAL BUG CORRECTION
o 1.19.2 Update Metadata from Ensembl function to use
GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP instead of parsing the
file path
o 1.19.1 misplaced ! clause
CHANGES IN VERSION 1.17.0
------------------------
MODIFICATIONS
o 1.17.3 add check for valid Title and Description in metadata file. It
should not be empty or NA
o 1.17.2 add XML as valid source type
o 1.17.1 add GSEMatrix as valid source type
CHANGES IN VERSION 1.15.0
------------------------
MODIFICATIONS
o 1.15.13 Added "BLOB" as a valid source type
o 1.15.7 Added "MTX" as a valid source type
o 1.15.6 Expanded documentation to clarify that data can be hosted
publically not strictly Bioconductor AWS
o 1.15.4 Added "XLS/XLSX" as valid source type
INTERNAL BUG CORRECTION
o 1.15.11 updated GencodeGFF recipes for potential future use (still would
revisit this with another update to do like ensembl on the fly)
o 1.15.5 remove validity check that is wrong/outdated
o 1.15.1 needToRerunNonStandardOrgDb added as helper function for when
generating non standard org dbs. 1.15.3 added try catch in case aws buckets
unreachable.
CHANGES IN VERSION 1.13.0
------------------------
NEW FEATURES
o Added ability to have multiple RDataPaths associated with single hub
id for strongly associated files (like bam and its bai index file)
o DispatchClass are now validated against AnnotationHub::DispatchClassList()
which contains currently available DispatchClass and brief description of
loading process.
CHANGES IN VERSION 1.11.0
------------------------
MODIFICATIONS
o Removed scripts for Pazar DB as website no longer active
o Update from BiocInstaller to BiocManager
NEW FEATURES
o Species and taxonomyId are now validated against GenomeInfoDbData object
BUG FIX
o Fix TwoBit resource receipe. Converts DNA that is not A,C,T,G,N to N do to
design of rtracklayer::export for TwoBit
o Fix bug with assignment of tags in annotationhub
o makeEpigenomeRoadMap recipe updated to account for XML bug that cannot
handle http urls. updated to https
CHANGES IN VERSION 1.10.0
------------------------
MODIFICATIONS
o Moved readMetadataFromCsv back to AnnotationHubData.
o Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv
o readMetadataFromCsv is now internal function
CHANGES IN VERSION 1.8.0
------------------------
NEW FEATURES
o Instead of using dropbox or ftp to deliver contributed resources to
Bioconductor Core, temporary access to Annotation-Contributor user on S3 is
utilized.
MODIFICATIONS
o Modified readMetadataFromCsv; make RDataPath mandatory entry and if
location_prefix is Bioconductor S3 bucket the Rdatapath must start with the
package name
BUG FIXES
o Add garbage collection to fix twobit memory allocation error
o Fix files not deleting do to special characters in file names
o Import dbGetQuery from DBI
o Remove hard coded biocVersion in unit tests
CHANGES IN VERSION 1.6.0
------------------------
NEW FEATURES
o add makeStandardTxDbsToSqlite() recipe
o add 'ensembl' and 'MySQL' as possible SourceType values
o tidy and export makeStandard*ToAHMs and makeNCBIToOrgDbsToAHMs
MODIFICATIONS
o move currentMetadata
o tidy pushResources interface
o modified parsing of species name and genome in .ensemblMetadataFromUrl()
o modified standard OrgDb recipe
o enhance and clean vignette
o move 'Tags' check from readCsvFromMetadata() to
makeAnnotationHubMetadata()
o remove dependency on xml2, curl, httr and probably other wheel
reinventions, alter imports and suggests
o specify multiple 'Tags' as colon separated string instead of comma
separated; avoids problems with read.csv()
o select data moved to GenomeInfoDbData package
o Added additional documentation instructions for core members to add
contributed data to AnnotationHub
o rename files; remove old JSON test file no longer applicable
o pass 'install' argument down through recipe
o General code tidy; remove unused functions and comments; clarify checks
BUG FIXES
o readMetadataFromCsv() fills in DataProvider and Coordinate_1_based if missing
o fix bug introduced in checking 'release' in makeEnsemblTwoBit recipe
o makeAnnotationHubMetadata() now processes all inst/extdata/*.csv files
o fix subset and import bug in makeAnnotationHubMetadata()
o Fix bug in Rdatapath and sourceurl for makeEnsemblFasta.R
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