2018-11-20 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix "version_avaliable" to "version_available"

2018-11-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* change samtools and htslib source_url t codeload
		* add the second source url of gridss 

2018-11-11 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* improve the sort method of versions
		* remove check_shiny_dep
		* use pacman to install the shiny application required packages
		* add shiny/deps.R to install the Shiny application dependences

2018-10-29 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* support bitbucket repo
		* add workflow tools and databases

2018-09-23 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* update ANNOVAR dbnsfp versions

2018-09-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add fill = TRUE in conda.list read.table

2018-08-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add copy_plugins and copy_configs functions in R/web.R
		* replace getURL by fromJSON to access the Github APIs

2018-08-18 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add miniconda and spack in docker image
		* add table output box in instant spack

2018-08-16 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add pubmed search tool
		* add geoquery instant plugin
		* improve instant spack and code plugins

2018-08-15 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add datasets2tools plugin

2018-08-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add wrapper functions, conda and spack
		* add new function new.bioinfo

2018-08-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* use editor in pipeline
		* add instant page
		* plugins dir could change

2018-08-02 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Improve the setting function
		* Use codemirror editor

2018-08-01 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Add setting UI in Shiny
		* rename craw.all.versions to crawl.all.versions

2018-07-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Add easy_project plugin in pipeline
		* Add files_of_path_monitor plugin in dashbord

2018-07-21 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Initial Shiny application

2018-05-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* design the BioInstaller logo
		* use pkgdown to generate document html site
		* update README.md and improve vignettes

2018-04-29 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add picky, freec, oncodriveclust, sequenza, taxmaps, 
		svaba, rop in github.toml
		* add jaffa_reffa in nongithub.toml 

2018-04-29 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* change db_annovar sql2sqlite parameter names
		* add manta and JAFFA in github.toml
		* add JAFFA reffa in nongithub.toml
		* update vignettes theme using prettydoc

2018-03-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add db_annovar_abraom

2018-01-20 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* added mutsig in nongithub

2018-01-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* added db_annovar_docm, db_annovar_intogen, 
		db_annovar_disgenet, db_annovar_cancer_hotspots in db
		* rename db_cancer_hotspot to db_cancer_hotspots
		* added RESM, radia in github
		* added rMATS, PARADA, IGV, Marina, PARADIGM, Meerkat, 
		vadir, in nongithub
		* source parse_version.R in local env

2018-01-10 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* added facets, GIGGLE (genomic search engine) in github
		* added absolute, hapseg, atlas2, beagle, contest 
		in nongithub

2018-01-09 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* added olego, chronqc and rHAT
		* set.biosoftwares.db(tempfile()) in vignettes/BioInstaller.Rmd

2018-01-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix CRAN warning, demo source_url modified 

2018-01-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* added db_rbp_var, db_docm, db_cancer_hotspot, 
		db_intogen, db_disgenet, db_cgi

2017-12-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix a bug if set save.to.db to FALSE

2017-12-15 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* reduce blank rows in config files

2017-12-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* update bcl2fastq source_url
		* add db_annovar_dbscsnv_sqlite

2017-12-12 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add vcfanno

2017-12-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add db_annovar_tall_somatic_genes
		* add db_eggnog

2017-12-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix a bug in craw.all.versions
		* db_rddpred, db_lncediting and its sqlite version be added
		* rename licence to license, add license paramter

2017-12-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_snipa3 be added
		* db_annovar_seeqtl be added
		* db_annovar_eqtl_egenes be added

2017-12-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_annovar_rediportal_sqlite, db_annovar_gme_sqlite,
		db_annovar_hrcr1_sqlite, db_annovar_revel_sqlite,
		db_annovar_mcap_sqlite, db_annovar_exac03_sqlite,
		db_annovar_gnomad_sqlite, db_annovar_popfreq_sqlite,
		db_annovar_gwava_sqlite, db_annovar_eigen_sqlite be added
		* db_exsnp, db_rvarbase and db_seeqtl be added
		* rename source_is.dir to source_is_dir
		* add dir download support for html page (previous only for ftp)

2017-12-02 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_annovar_loftool_score, db_annovar_rvis_esv_score, 
		db_annovar_gdi_score and db_annovar_tmcsnpdb be added 

2017-12-01 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_atcircdb, db_circnet, db_circbase, db_circrnadb, 
		and db_exorbase be added

2017-11-30 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* 1285 cases B-ALL RNA-seq variants database be added (resource not
		available)

2017-11-29 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_hgnc and db_annovar_hgnc be added

2017-11-27 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_annovar_varcards_sqlite be added

2017-11-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_tumorfusions and db_gtex be added

2017-11-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_expression_atlas,db_remap and db_remap2 be added
		* db_annovar_epi_genes, db_annovar_cscd be added
		* fix undecompressed filetype not move to destdir if set decompress to
		TRUE
		* interproscan be added
		* db_funcoup, db_proteinatlas, db_dgidb, db_drugbank, db_interpro,
		db_inbiomap, db_omim, db_biosystems, db_denovo_db and db_hpo be added

2017-11-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* use configr fetch.config to merge multiple github.cfg and
		nongithub.cfg

2017-11-21 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* db_ecodrug, db_medreaders, db_superdrug2, db_varcards be added
		* db_civic be added (only nightly)

2017-11-08 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix a bug in R/utils_function.R drop_redundance_dir
		* db_msdd, db_mndr be added in db/db_main.toml

2017-11-07 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* use_git_versions can be used in nongithub.toml to use github
		release versions
		* gridss, db_pancanqtl, db_seecancer and db_diseaseenhancer be supported
		* fix cfg_dir and prefix_url in inst/config/ meta files
		* JhuangLab provide ANNOVAR database sqlite files in db_annovar.toml
		* update avsnp150 and clinvar_20170905 be added in db_annovar.toml

2017-11-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* big change on path of toml files
		* move files from inst/extdata to inst/extdata/config, demo, scripts

2017-11-02 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* inst/extdata/web/web_meta.toml be added
		* Function get.meta.files and get.meta be added in 
		R/meta.R
		* Makefile be added
		* blast be supported

2017-11-01 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* URLencode be used
		* filenames in inst/extdata/databases changed, ANNOVAR.toml => db_annovar.toml, blast.toml =>
		db_blast.toml, meta.toml => db_meta.toml, main.toml => db_main.toml
		* prefix of database rename to db_.*, e.g. raw_ucsc_refseq =>
		db_ucsc_refseq in inst/extdata/databases/db_annovar.toml
		* inst/extdata/databases/CSCD.toml merged with db_main.toml
		* sRNAnalyzer, db_sRNAnalyzer, db_differentialnet be supported
		in db_main.toml

2017-10-31 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* aRNApipe, trim_galore, multiqc, ngs_qc_toolkit be supported 

2017-10-12 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* CSCD database be supported
		(/inst/extdata/databases/cscd.toml)

2017-10-09 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* strelka be added 
		* mm9/mm10 be added in ucsc_reffa
		* fix samtools-1.6 fail

2017-09-18 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix invalid test link
		* ANNOVAR databases can be download use
		inst/extdata/databases/ANNOVAR.toml
		* Move databases toml file to inst/extdata/databases/
		* DRAT and fastq-tools be added

2017-07-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* picard/mutect be added in inst/extdata/docker.toml

2017-07-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
		
		* craw.all.versions be add in R/craw.R
		* local.source be supported

2017-07-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* docker.pull and docker.search be added in R/docker.R
		* miniconda be supported

2017-06-25 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* oncotator be supported
		* VEP be supported
		* `decompress` in configuration file be processed by as.logical

2017-06-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Fix windows install status
		* 'Meta Infmation of Softwares and Databases' project initial

2017-06-23 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Cancel windows install step (Download still work)

2017-06-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Use v0.3.0 configr: glue parse be supported
		* inst/extdata/nongithub_databases_blast.toml be added
		* inst/extdata/nongithub_databases_meta.toml be added

2017-06-09 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Reduce the redundant step of extra files copy

2017-06-08 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* multiple line of #R# CMD can be parsed

2017-06-07 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* sleuth be supported (Differential analysis of RNA-Seq data)
		* add no.need.download option in github.toml to control no download
		from github url (e.g. use devtools to install)

2017-06-07 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* #R# RCMD #R# can be run in configuration file

2017-06-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
		
		* extra.list, rcmd.parse and bash.parse, save.to.db parameters be added in
		R/install.R install.bioinfo, install.github, install.nongithub
		* show.all.versions be improved

2017-06-01 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Non-Github softwares versions can be parsed from cfg or a parse function
		* version_newest_fixed can be added

2017-05-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Github softwares fetching versions by github API

2017-05-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Unittest be added
		* verbose default set TRUE, and log infomation be improved

2017-05-09 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
		
		* Use environment variable BIO_DEPENDENCE_DIR to set the download.dir and
		destdir of dependence softwares

2017-05-07 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* pcre URL FTP => HTTPS
		* Update R-3.4.0 install and download

2017-05-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* dependence.need parameters be added

2017-05-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* download.dir be supported
		* install.dir be saved in softwares info configuration file

2017-04-30 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* cnvkit be supported
		* eval.config.groups replaced by eval.config.sections

2017-04-27 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* bwa@0.7.2a => name.saved="bwa_0.7.2a"
		* ROOT/cnvnator/svtoolkit be supported download

2017-04-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
		
		* Update FastQC URL
		* Update Version newest
		* Change dependece install dir in the {{destdir}}/dependence/some_dependence
		* Add "softwares_version" format name recognition, eg. bwa@0.7.2a,
		name.saved="bwa@0.7.2a", version=0.7.2a
		* Release 0.1.0

2017-04-11 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* bcl2fastq2 be supported

2017-04-09 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* samstat, PRINSEQ, SolexaQA, fastx_toolkit be supported

2017-03-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
		
		* GATK, Mutect, SSAHA2, NovoAlign be supported
