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ChangeLog
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2018-08-03 Li Jianfeng <[email protected]>
* use editor in pipeline
* add instant page
* plugins dir could change
2018-08-02 Li Jianfeng <[email protected]>
* Improve the setting function
* Use codemirror editor
2018-08-01 Li Jianfeng <[email protected]>
* Add setting UI in Shiny
* rename craw.all.versions to crawl.all.versions
2018-07-22 Li Jianfeng <[email protected]>
* Add easy_project plugin in pipeline
* Add files_of_path_monitor plugin in dashbord
2018-07-21 Li Jianfeng <[email protected]>
* Initial Shiny application
2018-05-04 Li Jianfeng <[email protected]>
* design the BioInstaller logo
* use pkgdown to generate document html site
* update README.md and improve vignettes
2018-04-29 Li Jianfeng <[email protected]>
* add picky, freec, oncodriveclust, sequenza, taxmaps,
svaba, rop in github.toml
* add jaffa_reffa in nongithub.toml
2018-04-29 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* add db_annovar_abraom
2018-01-20 Li Jianfeng <[email protected]>
* added mutsig in nongithub
2018-01-19 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* added facets, GIGGLE (genomic search engine) in github
* added absolute, hapseg, atlas2, beagle, contest
in nongithub
2018-01-09 Li Jianfeng <[email protected]>
* added olego, chronqc and rHAT
* set.biosoftwares.db(tempfile()) in vignettes/BioInstaller.Rmd
2018-01-05 Li Jianfeng <[email protected]>
* fix CRAN warning, demo source_url modified
2018-01-03 Li Jianfeng <[email protected]>
* added db_rbp_var, db_docm, db_cancer_hotspot,
db_intogen, db_disgenet, db_cgi
2017-12-19 Li Jianfeng <[email protected]>
* fix a bug if set save.to.db to FALSE
2017-12-15 Li Jianfeng <[email protected]>
* reduce blank rows in config files
2017-12-13 Li Jianfeng <[email protected]>
* update bcl2fastq source_url
* add db_annovar_dbscsnv_sqlite
2017-12-12 Li Jianfeng <[email protected]>
* add vcfanno
2017-12-06 Li Jianfeng <[email protected]>
* add db_annovar_tall_somatic_genes
* add db_eggnog
2017-12-05 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* db_snipa3 be added
* db_annovar_seeqtl be added
* db_annovar_eqtl_egenes be added
2017-12-03 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* db_annovar_loftool_score, db_annovar_rvis_esv_score,
db_annovar_gdi_score and db_annovar_tmcsnpdb be added
2017-12-01 Li Jianfeng <[email protected]>
* db_atcircdb, db_circnet, db_circbase, db_circrnadb,
and db_exorbase be added
2017-11-30 Li Jianfeng <[email protected]>
* 1285 cases B-ALL RNA-seq variants database be added (resource not
available)
2017-11-29 Li Jianfeng <[email protected]>
* db_hgnc and db_annovar_hgnc be added
2017-11-27 Li Jianfeng <[email protected]>
* db_annovar_varcards_sqlite be added
2017-11-26 Li Jianfeng <[email protected]>
* db_tumorfusions and db_gtex be added
2017-11-24 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* use configr fetch.config to merge multiple github.cfg and
nongithub.cfg
2017-11-21 Li Jianfeng <[email protected]>
* db_ecodrug, db_medreaders, db_superdrug2, db_varcards be added
* db_civic be added (only nightly)
2017-11-08 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* big change on path of toml files
* move files from inst/extdata to inst/extdata/config, demo, scripts
2017-11-02 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* aRNApipe, trim_galore, multiqc, ngs_qc_toolkit be supported
2017-10-12 Li Jianfeng <[email protected]>
* CSCD database be supported
(/inst/extdata/databases/cscd.toml)
2017-10-09 Li Jianfeng <[email protected]>
* strelka be added
* mm9/mm10 be added in ucsc_reffa
* fix samtools-1.6 fail
2017-09-18 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* picard/mutect be added in inst/extdata/docker.toml
2017-07-24 Li Jianfeng <[email protected]>
* craw.all.versions be add in R/craw.R
* local.source be supported
2017-07-22 Li Jianfeng <[email protected]>
* docker.pull and docker.search be added in R/docker.R
* miniconda be supported
2017-06-25 Li Jianfeng <[email protected]>
* oncotator be supported
* VEP be supported
* `decompress` in configuration file be processed by as.logical
2017-06-24 Li Jianfeng <[email protected]>
* Fix windows install status
* 'Meta Infmation of Softwares and Databases' project initial
2017-06-23 Li Jianfeng <[email protected]>
* Cancel windows install step (Download still work)
2017-06-22 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* Reduce the redundant step of extra files copy
2017-06-08 Li Jianfeng <[email protected]>
* multiple line of #R# CMD can be parsed
2017-06-07 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* #R# RCMD #R# can be run in configuration file
2017-06-03 Li Jianfeng <[email protected]>
* 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 <[email protected]>
* Non-Github softwares versions can be parsed from cfg or a parse function
* version_newest_fixed can be added
2017-05-24 Li Jianfeng <[email protected]>
* Github softwares fetching versions by github API
2017-05-19 Li Jianfeng <[email protected]>
* Unittest be added
* verbose default set TRUE, and log infomation be improved
2017-05-09 Li Jianfeng <[email protected]>
* Use environment variable BIO_DEPENDENCE_DIR to set the download.dir and
destdir of dependence softwares
2017-05-07 Li Jianfeng <[email protected]>
* pcre URL FTP => HTTPS
* Update R-3.4.0 install and download
2017-05-04 Li Jianfeng <[email protected]>
* dependence.need parameters be added
2017-05-03 Li Jianfeng <[email protected]>
* download.dir be supported
* install.dir be saved in softwares info configuration file
2017-04-30 Li Jianfeng <[email protected]>
* cnvkit be supported
* eval.config.groups replaced by eval.config.sections
2017-04-27 Li Jianfeng <[email protected]>
* [email protected] => name.saved="bwa_0.7.2a"
* ROOT/cnvnator/svtoolkit be supported download
2017-04-24 Li Jianfeng <[email protected]>
* Update FastQC URL
* Update Version newest
* Change dependece install dir in the {{destdir}}/dependence/some_dependence
* Add "softwares_version" format name recognition, eg. [email protected],
name.saved="[email protected]", version=0.7.2a
* Release 0.1.0
2017-04-11 Li Jianfeng <[email protected]>
* bcl2fastq2 be supported
2017-04-09 Li Jianfeng <[email protected]>
* samstat, PRINSEQ, SolexaQA, fastx_toolkit be supported
2017-03-19 Li Jianfeng <[email protected]>
* GATK, Mutect, SSAHA2, NovoAlign be supported