v0.3.3

Author: Miachol

ChangeLog

@@ -1,3 +1,7 @@
+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, 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioInstaller
 Title: Lightweight Biology Software Installer
-Version: 0.3.2.3
+Version: 0.3.3
 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.

NEWS.md

@@ -0,0 +1,13 @@
+# BioInstaller v0.3.3
+
+## Softwares
+
+- Supported 148 softwares
+
+## Databases
+
+- Supported 169 databases
+
+## Bug Fixed
+
+- Fixed a bug when set save.to.db to FALSE. It can raise installed fail

R/info.R

@@ -5,7 +5,7 @@
 #' @param source.dir Directorie of softwares source code
 #' @param bin.dir Directorie of softwares bin
 #' @param executable.files Executable files in bin.dir
-#' @param db File of saving softwares infomation
+#' @param db File saving softwares infomation
 #' @param ... Other key and value paired need be saved in BioInstaller
 #' @param verbose Ligical indicating wheather show the log message
 #' @export
@@ -17,8 +17,7 @@
 #' bin.dir = '', excutable.files = c('demo'), others.customer = 'demo')
 #' unlink(db)
 change.info <- function(name = "", installed = TRUE, source.dir = "", bin.dir = "", 
-  executable.files = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", system.file("extdata", 
-    "demo/softwares_db_demo.yaml", package = "BioInstaller")), ..., verbose = TRUE) {
+  executable.files = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), ..., verbose = TRUE) {
   msg <- sprintf("Running change.info for %s and be saved to %s", name, db)
   info.msg(msg, verbose = verbose)
   source.dir <- normalizePath(source.dir, mustWork = F)
@@ -40,7 +39,7 @@ change.info <- function(name = "", installed = TRUE, source.dir = "", bin.dir =
 #' Show biologly softwares infomation of system
 #'
 #' @param name Software name
-#' @param db File of saving softwares infomation
+#' @param db File saving softwares infomation
 #' @param verbose Ligical indicating wheather show the log message
 #' @export
 #' @return Bool Value
@@ -51,8 +50,7 @@ change.info <- function(name = "", installed = TRUE, source.dir = "", bin.dir =
 #' bin.dir = '', excutable.files = c('demo'), others.customer = 'demo')
 #' get.info('bwa')
 #' unlink(db)
-get.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", system.file("extdata", 
-  "demo/softwares_db_demo.yaml", package = "BioInstaller")), verbose = TRUE) {
+get.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), verbose = TRUE) {
   db <- normalizePath(db, mustWork = FALSE)
   if (!db.check(db)) {
     return(FALSE)
@@ -72,7 +70,7 @@ get.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", syste
 #' Delete biologly softwares infomation of system
 #'
 #' @param name Software name
-#' @param db File of saving softwares infomation
+#' @param db File saving softwares infomation
 #' @param verbose Ligical indicating wheather show the log message
 #' @export
 #' @return Bool Value
@@ -83,8 +81,7 @@ get.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", syste
 #' bin.dir = '', excutable.files = c('demo'), others.customer = 'demo')
 #' del.info('bwa')
 #' unlink(db)
-del.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", system.file("extdata", 
-  "demo/softwares_db_demo.yaml", package = "BioInstaller")), verbose = TRUE) {
+del.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), verbose = TRUE) {
   db <- normalizePath(db, mustWork = FALSE)
   if (!db.check(db)) {
     return(FALSE)
@@ -104,7 +101,7 @@ del.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", syste
 
 #' Show all installed bio-softwares in system
 #'
-#' @param db File of saving softwares infomation
+#' @param db File saving softwares infomation
 #' @param only.installed Logical wheather only show installed softwares in db
 #' @param verbose Ligical indicating wheather show the log message
 #' @export
@@ -116,8 +113,7 @@ del.info <- function(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", syste
 #' bin.dir = '', excutable.files = c('demo'), others.customer = 'demo')
 #' show.installed()
 #' unlink(db)
-show.installed <- function(db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", system.file("extdata", 
-  "demo/softwares_db_demo.yaml", package = "BioInstaller")), only.installed = TRUE, 
+show.installed <- function(db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), only.installed = TRUE, 
   verbose = TRUE) {
   db <- normalizePath(db, mustWork = FALSE)
   if (!db.check(db)) {

inst/extdata/config/nongithub/nongithub.toml

@@ -198,7 +198,7 @@ linux = ["mkdir -p {{destdir}}/bin; fn=`ls -F bin|grep '*' | tr -d '*'` ;cd bin;
 mac = ["mkdir -p {{destdir}}/bin; fn=`ls -F bin|grep '*' | tr -d '*'` ;cd bin;", " cp $fn {{destdir}}/bin"]
 
 [fusioncatcher]
-source_url = ["https://sourceforge.net/projects/fusioncatcher/files/fusioncatcher_{{version}}.zip", 
+source_url = ["https://sourceforge.net/projects/fusioncatcher/files/fusioncatcher_{{version}}.zip",
               "https://sourceforge.net/projects/fusioncatcher/files/bootstrap.py"]
 decompress = [true, false]
 #dependence = ["bwa", "blat", "faToTwoBit", "bowtie", "bowtie2", "star", "sratools", "velvet", "lzo", "pigz", "seqtk", "picard", "samtools_old", "pxz", "liftover"]
@@ -304,7 +304,7 @@ version_available = ["1.2.11", "1.2.10", "1.2.9", "1.2.7", "1.2.8", "1.2.6", "1.
 make_dir = ["./"]
 bin_dir = ["{{destdir}}/lib"]
 
-[zlib.source_url] 
+[zlib.source_url]
 linux = ["https://sourceforge.net/projects/libpng/files/zlib/{{version}}/zlib-{{version}}.tar.gz"]
 mac = ["https://sourceforge.net/projects/libpng/files/zlib/{{version}}/zlib-{{version}}.tar.gz"]
 
@@ -543,18 +543,18 @@ bin_dir = ["{{destdir}}/bin"]
 url_all_download = false
 
 [r.source_url]
-linux = ["https://cran.r-project.org/src/base/R-3/R-{{version}}.tar.gz", 
-              "https://cran.r-project.org/src/base/R-2/R-{{version}}.tar.gz", 
-              "https://cran.r-project.org/src/base/R-1/R-{{version}}.tgz", 
+linux = ["https://cran.r-project.org/src/base/R-3/R-{{version}}.tar.gz",
+              "https://cran.r-project.org/src/base/R-2/R-{{version}}.tar.gz",
+              "https://cran.r-project.org/src/base/R-1/R-{{version}}.tgz",
               "https://cran.r-project.org/src/base/R-0/R-{{version}}.tgz"]
-mac = ["https://cran.r-project.org/bin/macosx/R-{{version}}.pkg", 
+mac = ["https://cran.r-project.org/bin/macosx/R-{{version}}.pkg",
        "https://cran.r-project.org/bin/macosx/old/R-{{version}}.pkg"]
-windows = ["https://cran.r-project.org/bin/windows/base/R-{{version}}-win.exe", 
+windows = ["https://cran.r-project.org/bin/windows/base/R-{{version}}-win.exe",
            "https://cran.r-project.org/bin/windows/base/old/{{versions}}/R-{{version}}-win.exe"]
 
 [r.install]
 linux = ["""./configure --enable-R-shlib --prefix={{destdir}} CFLAGS='\
-@>@ 
+@>@
 library(stringr)
 include.flag <- unique(c('-I{{zlib:install.dir}}/include', '-I{{bzip2:install.dir}}/include', '-I{{xz:install.dir}}/include', '-I{{pcre:install.dir}}/include', '-I{{curl:install.dir}}/include'))
 include.flag <- include.flag[!str_detect(include.flag, ':')]
@@ -564,11 +564,11 @@ LDFLAGS='\
 @>@
 lib.flag <- unique(c('-I{{zlib:install.dir}}/lib', '-I{{bzip2:install.dir}}/lib', '-I{{xz:install.dir}}/lib', '-I{{pcre:install.dir}}/lib', '-I{{curl:install.dir}}/lib'))
 lib.flag <- lib.flag[!str_detect(lib.flag, ':')]
-paste(lib.flag, collapse=' ') 
+paste(lib.flag, collapse=' ')
 @<@' \
 && make""", "make install"]
 mac = ["""./configure --enable-R-shlib --prefix={{destdir}} CFLAGS='\
-@>@ 
+@>@
 library(stringr)
 include.flag <- unique(c('-I{{zlib:install.dir}}/include', '-I{{bzip2:install.dir}}/include', '-I{{xz:install.dir}}/include', '-I{{pcre:install.dir}}/include', '-I{{curl:install.dir}}/include'))
 include.flag <- include.flag[!str_detect(include.flag, ':')]
@@ -578,7 +578,7 @@ LDFLAGS='\
 @>@
 lib.flag <- unique(c('-I{{zlib:install.dir}}/lib', '-I{{bzip2:install.dir}}/lib', '-I{{xz:install.dir}}/lib', '-I{{pcre:install.dir}}/lib', '-I{{curl:install.dir}}/lib'))
 lib.flag <- lib.flag[!str_detect(lib.flag, ':')]
-paste(lib.flag, collapse=' ') 
+paste(lib.flag, collapse=' ')
 @<@' \
 && make""", "make install"]
 
@@ -593,8 +593,8 @@ mac = "pip install ."
 decompress = false
 url_all_download = false
 
-[miniconda2.source_url] 
-windows = ["https://repo.continuum.io/miniconda/Miniconda2-{{version}}-Windows-x86_64.exe", 
+[miniconda2.source_url]
+windows = ["https://repo.continuum.io/miniconda/Miniconda2-{{version}}-Windows-x86_64.exe",
            "http://bioinfo.rjh.com.cn/download/miniconda/Miniconda2-{{version}}-Windows-x86_64.exe"]
 mac = ["https://repo.continuum.io/miniconda/Miniconda2-{{version}}-MacOSX-x86_64.sh",
        "http://bioinfo.rjh.com.cn/download/miniconda/Miniconda2-{{version}}-MacOSX-x86_64.sh"]
@@ -610,7 +610,7 @@ decompress = false
 url_all_download = false
 
 [miniconda3.source_url]
-windows = ["https://repo.continuum.io/miniconda/Miniconda3-{{version}}-Windows-x86_64.exe", 
+windows = ["https://repo.continuum.io/miniconda/Miniconda3-{{version}}-Windows-x86_64.exe",
            "http://bioinfo.rjh.com.cn/download/miniconda/Miniconda3-{{version}}-Windows-x86_64.exe"]
 mac = ["https://repo.continuum.io/miniconda/Miniconda3-{{version}}-MacOSX-x86_64.sh",
        "http://bioinfo.rjh.com.cn/download/miniconda/Miniconda3-{{version}}-MacOSX-x86_64.sh"]
@@ -624,7 +624,7 @@ mac = "sh Miniconda3-{{version}}-MacOSX-x86_64.sh"
 [strelka]
 source_url = "ftp://strelka@ftp.illumina.com/v1-branch/v{{version}}/strelka_workflow-{{version}}.tar.gz"
 version_order_fixed = true
-version_available = ["1.0.15", "1.0.4", "1.0.5", "1.0.6", "1.0.7", "1.0.10", 
+version_available = ["1.0.15", "1.0.4", "1.0.5", "1.0.6", "1.0.7", "1.0.10",
                      "1.0.11", "1.0.12", "1.0.13", "1.0.14"]
 
 [strelka.install]
@@ -644,7 +644,7 @@ version_available = "latest"
 version_available = ["2.7.1", "2.6.0", "2.5.0", "2.4.0", "2.3.0"]
 [blast.source_url]
 linux = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+-x64-linux.tar.gz"
-mac = ["ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+-x64-macosx.tar.gz", 
+mac = ["ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+-x64-macosx.tar.gz",
        "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+.dmg"]
 win = ["ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+-x64-win64.tar.gz",
        "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+-win64.exe"]
@@ -658,7 +658,7 @@ mac = "mkdir -p {{destdir}}/bin; cp {{download.dir}}/*.jar {{destdir}}/bin"
 
 [interproscan]
 source_url = [
-              "ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/{{version}}/interproscan-{{version}}-64-bit.tar.gz", 
+              "ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/{{version}}/interproscan-{{version}}-64-bit.tar.gz",
               "http://bioinfo.rjh.com.cn/download/bioinstaller/interproscan/interproscan-{{version}}-64-bit.tar.gz"
 ]
 url_all_download = false
@@ -675,7 +675,7 @@ make_dir = ["./src"]
 linux = "make -f Makefile.Linux"
 mac = "make -f Makefile.MacOS"
 
-[vcfanno.source_url] 
+[vcfanno.source_url]
 linux = "https://github.com/brentp/vcfanno/releases/download/{{version}}/vcfanno_linux64"
 mac = "https://github.com/brentp/vcfanno/releases/download/{{version}}/vcfanno_osx"
 [vcfanno]
@@ -706,11 +706,11 @@ version_available = ["1.4.3", "1.4.1"]
 
 [beagle]
 source_url = "http://faculty.washington.edu/browning/beagle/{{version}}"
-version_available = ["beagle.08Jun17.d8b.jar", "beagle_4.1_21Jan17.pdf", "run.beagle.08Jun17.d8b.example", 
+version_available = ["beagle.08Jun17.d8b.jar", "beagle_4.1_21Jan17.pdf", "run.beagle.08Jun17.d8b.example",
                      "release_notes", "beagle.170608.zip"]
 
 [contest]
-source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/contest/contest-{{version}}-bin.zip", 
+source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/contest/contest-{{version}}-bin.zip",
               "hg19_population_stratified_af_hapmap_3.3.vcf.gz"]
 url_all_download = true
 version_available = "1.0.24530"
@@ -747,6 +747,18 @@ source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/meerkat/meerkat.{{
 version_available = "0.189"
 
 [vadir]
-source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/vadir/VaDiR.tar.gz", 
+source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/vadir/VaDiR.tar.gz",
               "ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/VaDiR.tar.gz"]
 version_available = "latest"
+
+[mutsig]
+source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/mutsig/MutSigCV_{{version}}.zip"
+version_available = ["1.41"]
+
+[mutsig_dependence]
+source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/mutsig/{{version}}.zip"
+version_available = ["exome_full192.coverage", "mutation_type_dictionary_file.txt"]
+
+[mutsig_reffa]
+source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/mutsig/{{version}}.zip"
+version_available = ["hg19.fa"]

inst/extdata/config/nongithub/nongithub_meta.toml

@@ -122,3 +122,10 @@ level. We also found that the integration of Tier1 variants with those called by
 the highest recall with acceptable precision. Finally, we observed higher rate of mutation discovery in genes
 that are expressed at higher levels."""
 publication = "Neums L, Suenaga S, Beyerlein P, et al. VaDiR: an integrated approach to Variant Detection in RNA[J]. GigaScience, 2017. https://doi.org/10.1093/gigascience/gix122"
+
+[nongithub.item.mutsig]
+title = "Mutational heterogeneity in cancer and the search for new cancer-associated genes"
+description = """
+MutSig (for "Mutation Significance") is a package of tools for analyzing mutation data.  It operates on a cohort of patients and identifies mutations, genes, and other genomic elements predicted to be driver candidates.
+"""
+publication = "Lawrence, M. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013) http://dx.doi.org/10.1038/nature12213"