Use canonical URL and add some of docker repo

JhuangLab · Jul 25, 2017 · 77c69d1 · 77c69d1
1 parent 0889b8b
commit 77c69d1
Show file tree

Hide file tree

Showing 4 changed files with 28 additions and 2 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,7 @@
+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

diff --git 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
@@ -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
@@ -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)
+```