making a new bgee release

Todo at each Bgee release.

Webapp

Files available

Server

• create a new alias for versioning queries made by the R package to the server, e.g.: http://r13_2.bgee.org/

FTP

• Update the TSV file release_v2.tsv, at the root of the FTP directory: this file contains the list of Bgee versions available, and the URLs to access them, in descending order of release (newest release first). This file is notably used by the R package. Example:

release	release date	FTP URL	TopAnat URL	Affymetrix annotation URL pattern	Affymetrix all value URL pattern	Affymetrix experiment value URL pattern	RNA-Seq annotation URL pattern	RNA-Seq all value URL pattern	RNA-Seq experiment value URL pattern	minimumVersionBgeeDB	messageToUsers
14.0	2018-02-21	ftp://ftp.bgee.org/bgee_v14_0/	https://r.bgee.org/	ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/affymetrix/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_Affymetrix_experiments_chips.tar.gz	ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/affymetrix/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_Affymetrix_probesets.tar.gz	ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/affymetrix/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_Affymetrix_probesets_EXPIDPATTERN.tar.gz	ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/rna_seq/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_RNA-Seq_experiments_libraries.tar.gz	ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/rna_seq/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_RNA-Seq_read_counts_TPM_FPKM.tar.gz	ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/rna_seq/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_RNA-Seq_read_counts_TPM_FPKM_EXPIDPATTERN.tsv.tar.gz	2.6.1	
13.2	2016-07-06	ftp://ftp.bgee.org/bgee_v13_2/	https://r.bgee.org/bgee13/	ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/affymetrix/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_Affymetrix_experiments_chips.zip	ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/affymetrix/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_Affymetrix_probesets.zip	ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/affymetrix/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_Affymetrix_probesets_EXPIDPATTERN.zip	ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_RNA-Seq_experiments_libraries.zip	ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_RNA-Seq_read_counts_RPKM.zip	ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/SPECIESNAMEPATTERN/SPECIESNAMEPATTERN_RNA-Seq_read_counts_RPKM_EXPIDPATTERN.tsv.zip	2.3.0	Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/

Column minimumVersionBgeeDB allows to define the oldest release of the R package compatible with one specific version of Bgee. According to the file given as example below, versions 2.6.0 or older of the R package can not access to Bgee 14.

Column messageToUsers allows to write a message to users when the R package is loaded. This message is written after the prefix IMPORTANT INFORMATION: . If this column is empty no message is written.

• Versions of the R package released before Bgee 14 use the TSV file release.tsv at the root of the FTP directory. This file should not be edited when a new version of the package is released. It should not be moved, or deleted.

R Package