From 46d7076ae574b1403291884e5aa48175c1a25110 Mon Sep 17 00:00:00 2001 From: Li Jianfeng Date: Wed, 24 Jan 2018 19:22:26 +0800 Subject: [PATCH] v0.3.3 --- ChangeLog | 4 ++ DESCRIPTION | 2 +- NEWS.md | 13 +++++ R/info.R | 20 +++---- inst/extdata/config/nongithub/nongithub.toml | 54 +++++++++++-------- .../config/nongithub/nongithub_meta.toml | 7 +++ man/change.info.Rd | 5 +- man/del.info.Rd | 7 ++- man/get.info.Rd | 7 ++- man/show.installed.Rd | 7 ++- 10 files changed, 77 insertions(+), 49 deletions(-) create mode 100644 NEWS.md diff --git a/ChangeLog b/ChangeLog index d308548..fee5e36 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,7 @@ +2018-01-20 Li Jianfeng + + * added mutsig in nongithub + 2018-01-19 Li Jianfeng * added db_annovar_docm, db_annovar_intogen, diff --git a/DESCRIPTION b/DESCRIPTION index 8e31861..e26c8b6 100644 --- a/DESCRIPTION +++ b/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. diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..f0ddb44 --- /dev/null +++ b/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 diff --git a/R/info.R b/R/info.R index 20a2a86..764767e 100644 --- a/R/info.R +++ b/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)) { diff --git a/inst/extdata/config/nongithub/nongithub.toml b/inst/extdata/config/nongithub/nongithub.toml index 25c00bd..1f3e081 100644 --- a/inst/extdata/config/nongithub/nongithub.toml +++ b/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"] diff --git a/inst/extdata/config/nongithub/nongithub_meta.toml b/inst/extdata/config/nongithub/nongithub_meta.toml index 8cfb660..1882082 100644 --- a/inst/extdata/config/nongithub/nongithub_meta.toml +++ b/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" diff --git a/man/change.info.Rd b/man/change.info.Rd index c145acd..8a34c18 100644 --- a/man/change.info.Rd +++ b/man/change.info.Rd @@ -6,8 +6,7 @@ \usage{ change.info(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) + tempfile()), ..., verbose = TRUE) } \arguments{ \item{name}{Software name} @@ -20,7 +19,7 @@ change.info(name = "", installed = TRUE, source.dir = "", bin.dir = "", \item{executable.files}{Executable files in bin.dir} -\item{db}{File of saving softwares infomation} +\item{db}{File saving softwares infomation} \item{...}{Other key and value paired need be saved in BioInstaller} diff --git a/man/del.info.Rd b/man/del.info.Rd index 2a39f6f..61a041d 100644 --- a/man/del.info.Rd +++ b/man/del.info.Rd @@ -4,14 +4,13 @@ \alias{del.info} \title{Delete biologly softwares infomation of system} \usage{ -del.info(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", - system.file("extdata", "demo/softwares_db_demo.yaml", package = - "BioInstaller")), verbose = TRUE) +del.info(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), + verbose = TRUE) } \arguments{ \item{name}{Software name} -\item{db}{File of saving softwares infomation} +\item{db}{File saving softwares infomation} \item{verbose}{Ligical indicating wheather show the log message} } diff --git a/man/get.info.Rd b/man/get.info.Rd index dbd0ab2..0d36206 100644 --- a/man/get.info.Rd +++ b/man/get.info.Rd @@ -4,14 +4,13 @@ \alias{get.info} \title{Show biologly softwares infomation of system} \usage{ -get.info(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", - system.file("extdata", "demo/softwares_db_demo.yaml", package = - "BioInstaller")), verbose = TRUE) +get.info(name = "", db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), + verbose = TRUE) } \arguments{ \item{name}{Software name} -\item{db}{File of saving softwares infomation} +\item{db}{File saving softwares infomation} \item{verbose}{Ligical indicating wheather show the log message} } diff --git a/man/show.installed.Rd b/man/show.installed.Rd index 8ab1c3d..bd46507 100644 --- a/man/show.installed.Rd +++ b/man/show.installed.Rd @@ -4,12 +4,11 @@ \alias{show.installed} \title{Show all installed bio-softwares in system} \usage{ -show.installed(db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", - system.file("extdata", "demo/softwares_db_demo.yaml", package = - "BioInstaller")), only.installed = TRUE, verbose = TRUE) +show.installed(db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", tempfile()), + only.installed = TRUE, verbose = TRUE) } \arguments{ -\item{db}{File of saving softwares infomation} +\item{db}{File saving softwares infomation} \item{only.installed}{Logical wheather only show installed softwares in db}