Merge branch 'develop'

JhuangLab · Sep 18, 2017 · 325ccb8 · 325ccb8
2 parents e856ef6 + 09825f7
commit 325ccb8
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,11 @@
+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

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: BioInstaller 
 Title: Lightweight Biology Software Installer
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: person("Jianfeng", "Li", email = "lee_jianfeng@sjtu.edu.cn", role = c("aut", "cre"))
 Description:
     Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
 Depends:
     R (>= 3.3.0)
-URL: https://github.com/JhuangLab/BioInstaller, http://bioinfo.rjh.com.cn/labs/jhuang/tools/BioInstaller
+URL: https://github.com/JhuangLab/BioInstaller
 BugReports: https://github.com/JhuangLab/BioInstaller/issues
 License: MIT + file LICENSE
 Encoding: UTF-8

diff --git a/inst/extdata/databases/ANNOVAR.toml b/inst/extdata/databases/ANNOVAR.toml
diff --git a/inst/extdata/nongithub_databases_blast.toml → inst/extdata/databases/blast.toml b/inst/extdata/nongithub_databases_blast.toml → inst/extdata/databases/blast.toml
diff --git a/inst/extdata/nongithub_databases.toml → inst/extdata/databases/main.toml b/inst/extdata/nongithub_databases.toml → inst/extdata/databases/main.toml
diff --git a/inst/extdata/nongithub_databases_meta.toml → inst/extdata/databases/meta.toml b/inst/extdata/nongithub_databases_meta.toml → inst/extdata/databases/meta.toml
diff --git a/inst/extdata/github.toml b/inst/extdata/github.toml
@@ -801,3 +801,17 @@ make_dir = "ensembl-vep"
 [vep.install]
 linux = 'perl INSTALL.pl'
 mac = 'perl INSTALL.pl'
+
+[dart]
+github_url = "https://github.com/hsinnan75/DART"
+
+[dart.install]
+linux = "make"
+mac = "make"
+
+[fastq_tools]
+github_url = "https://github.com/dcjones/fastq-tools"
+
+[fastq_tools.install]
+linux = ["sh autogen.sh && ./configure --prefix={{destdir}} && make", "make install"]
+mac = ["sh autogen.sh && ./configure --prefix={{destdir}} && make", "make install"]
diff --git a/inst/extdata/nongithub.toml b/inst/extdata/nongithub.toml
@@ -1,7 +1,7 @@
 # Configuration file of install.softwares(Non-Github)
 title = "Non-Github Configuration File"
 [demo]
-source_url = "http://bioinfo.rjh.com.cn/download/annovarR/humandb/{{version}}_MT_ensGene.txt"
+source_url = "https://github.com/Miachol/ftp/blob/master/files/{{version}}_MT_ensGene.txt"
 decompress = false
 url_all_download = false
 version_newest = "GRCh37"
@@ -12,7 +12,7 @@ make_dir = ["./"]
 bin_dir = ["./"]
 
 [demo_2]
-source_url = "http://bioinfo.rjh.com.cn/download/annovarR/humandb/{{version}}_MT_ensGene.txt.gz"
+source_url = "https://github.com/Miachol/ftp/blob/master/files/{{version}}_MT_ensGene.txt.gz"
 url_all_download = false
 version_newest = "GRCh37"
 version_available = ["GRCh37"]
@@ -229,7 +229,7 @@ linux = "python setup.py install"
 mac = "python setup.py install"
 
 [novoalign]
-source_url = ["http://bioinfo.rjh.com.cn/download/novocraft/novocraft{{version}}.tar.gz"]
+source_url = ["https://github.com/Miachol/novocraft_releases/raw/master/novocraft{{version}}.tar.gz"]
 
 version_newest = "V3.07.01.Linux3.0"
 
@@ -268,11 +268,11 @@ linux = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{des
 mac = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin"
 
 [gatk]
-source_url = ["http://bioinfo.rjh.com.cn/download/gatk/gatk{{version}}.tar.gz"]
+source_url = ["https://github.com/Miachol/gatk_releases/raw/master/gatk{{version}}.tar.gz"]
 
-version_newest = "3.7-0"
+version_newest = "3.8-0"
 
-version_available = ["3.7-0", "3.7", "3.6", "3.5", "3.4-46"]
+version_available = ["3.8-0", "3.7-0", "3.7", "3.6", "3.5", "3.4-46"]
 
 after_failure = "echo 'fail!'"
 
@@ -287,7 +287,7 @@ linux = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin"
 mac = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin"
 
 [mutect]
-source_url = ["http://bioinfo.rjh.com.cn/download/gatk/mutect{{version}}.zip"]
+source_url = ["https://github.com/Miachol/gatk_releases/raw/master/mutect{{version}}.zip"]
 
 version_newest = "1.1.7"
 

diff --git a/tests/testthat/test_utils.R b/tests/testthat/test_utils.R
@@ -99,7 +99,7 @@ test_that("get.file.type", {
 })
 
 test_that("download.file.custom", {
-  url <- "http://bioinfo.rjh.com.cn/download/annovarR/humandb/GRCh37_MT_ensGene.txt"
+  url <- "https://github.com/Miachol/ftp/blob/master/files/GRCh37_MT_ensGene.txt"
   destfile <- sprintf("%s/GRCh37", tempdir())
   x <- download.file.custom(url, destfile, quiet = T)
   expect_that(x, equals(0))

diff --git a/vignettes/BioInstaller.Rmd b/vignettes/BioInstaller.Rmd
@@ -61,7 +61,7 @@ download.dir <- sprintf('%s/demo_3', tempdir())
 install.bioinfo('demo', download.dir = download.dir,
   download.only = TRUE, verbose = TRUE)
 
-# Set download.dir rrr destdir (destdir like /usr/local 
+# Set download.dir and destdir (destdir like /usr/local 
 # including bin, lib, include and others), 
 # destdir will work if install step {{destdir}} be used
 download.dir <- sprintf('%s/demo_source', tempdir())
@@ -116,3 +116,13 @@ BioInstaller provide a `craw.all.version` function to try download all avaliable
 download.dir <- sprintf('%s/craw_all_versions', tempdir())
 craw.all.versions('demo', download.dir = download.dir)
 ```
+
+## Download ANNOVAR databases
+
+```{r}
+download.dir <- sprintf('%s/ANNOVAR', tempdir())
+config.toml <- system.file("extdata", "databases/ANNOVAR.toml", 
+  package = "BioInstaller")
+install.bioinfo('raw_ucsc_refgene', download.dir = download.dir, 
+  nongithub.cfg = config.toml, extra.list = list(buildver = "hg19"))
+```
diff --git a/vignettes/write_configuration_file.Rmd b/vignettes/write_configuration_file.Rmd
@@ -83,15 +83,15 @@ Version control of non-github softwares and databases need a function parsing UR
 
 ## nongithub_databases_blast.toml
 
-This configuration file can be used to download NCBI blast database: `install.bioinfo(nongithub.cfg = system.file('extdata', 'nongithub_databases_blast.toml', package = 'BioInstaller'), show.all.names = TRUE)`.
+This configuration file can be used to download NCBI blast database: `install.bioinfo(nongithub.cfg = system.file('extdata', 'databases/blast.toml', package = 'BioInstaller'), show.all.names = TRUE)`.
 
 BioInstaller use [configr](https://github.com/Miachol/configr) `glue` to reduce the length of files name. That using less word to storage more files name. More useful databases FTP url can be accessed in the future. I hope you can set your own configuration file not only use the BioInstaller built-in configuration files.
 
 ```{r}
 library(configr)
 library(BioInstaller)
 blast.databases <- system.file('extdata', 
-  'nongithub_databases_blast.toml', package = 'BioInstaller')
+  'databases/blast.toml', package = 'BioInstaller')
 
 read.config(blast.databases)$blast_db_nr$source_url
 read.config(blast.databases, glue.parse = TRUE)$blast_db_nr$source_url