diff --git a/ChangeLog b/ChangeLog index 0b147d3..95e6799 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,7 @@ +2017-07-24 Li Jianfeng + + * picard/mutect be added in inst/extdata/docker.toml + 2017-07-24 Li Jianfeng * craw.all.versions be add in R/craw.R diff --git a/README.md b/README.md index 6e92fca..16a9440 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ establish a complete set of softwares and dependent files and set the correspond BioInstaller can help us to download, install and manage a variety of bioinformatics tools and databases more easily and systematically. -What's more, BioInstaller provides a different way to download and install your files, softwares and databases for others, more detail can be found in another vignette [Examples of Templet Configuration File](https://cran.r-project.org/web/packages/BioInstaller/vignettes/write_configuration_file.html). +What's more, BioInstaller provides a different way to download and install your files, softwares and databases for others, more detail can be found in another vignette [Examples of Templet Configuration File](https://CRAN.R-project.org/package=BioInstaller/vignettes/write_configuration_file.html). **Feature**: diff --git a/inst/extdata/docker.toml b/inst/extdata/docker.toml index 4a2da9f..7095cf1 100644 --- a/inst/extdata/docker.toml +++ b/inst/extdata/docker.toml @@ -19,3 +19,17 @@ name = "samtools" version_newest = "latest" version_available = ["latest"] short_description = """samtools:Tools (written in C using htslib) for manipulating next-generation sequencing data""" + +[picard] +repo = ["life2cloud"] +name = "picard" +version_newest = "latest" +version_available = ["latest"] +short_description = """picard:A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.""" + +[mutect] +repo = ["life2cloud"] +name = "mutect" +version_newest = "latest" +version_available = ["latest"] +short_description = """mutect:Accurate and sensitive cancer mutation detection""" diff --git a/vignettes/BioInstaller.Rmd b/vignettes/BioInstaller.Rmd index 7ddbb0f..6e42f81 100644 --- a/vignettes/BioInstaller.Rmd +++ b/vignettes/BioInstaller.Rmd @@ -32,7 +32,7 @@ establish a complete set of softwares and dependent files and set the correspond BioInstaller can help us to download, install and manage a variety of bioinformatics tools and databases more easily and systematically. -What's more, BioInstaller provides a different way to download and install your files, softwares and databases for others, more detail can be found in another vignette [Examples of Templet Configuration File](https://cran.r-project.org/web/packages/BioInstaller/vignettes/write_configuration_file.html). +What's more, BioInstaller provides a different way to download and install your files, softwares and databases for others, more detail can be found in another vignette [Examples of Templet Configuration File](https://CRAN.R-project.org/package=BioInstaller/vignettes/write_configuration_file.html). **Feature**: @@ -108,3 +108,11 @@ install.bioinfo('demo_2', download.dir = download.dir, download.only = TRUE, ver install.bioinfo('demo_2', download.dir = download.dir, local.source = sprintf('%s/GRCh37_MT_ensGene.txt.gz', download.dir), decompress = TRUE) ``` +## Craw all versions of softwares or databases + +BioInstaller provide a `craw.all.version` function to try download all avaliable URL files in nongithub part. + +```{r} +download.dir <- sprintf('%s/craw_all_versions', tempdir()) +craw.all.versions('demo', download.dir = download.dir) +```