add miniconda and spack in docker image

ChangeLog

@@ -1,3 +1,8 @@
+2018-08-18 Li Jianfeng <[email protected]>
+
+		* add miniconda and spack in docker image
+		* add table output box in instant spack
+
 2018-08-16 Li Jianfeng <[email protected]>
 
 		* add pubmed search tool

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioInstaller
 Title: Integrator of Bioinformatics Resources
-Version: 0.3.5.6000
+Version: 0.3.5.7000
 Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Maintainer: Jianfeng Li <[email protected]>
 Description:

Dockerfile

@@ -5,18 +5,27 @@ MAINTAINER "Jianfeng Li" [email protected]
 
 ADD . /tmp/BioInstaller
 
-Run apt update && apt install -y lmodern \
+Run apt update && apt install -y lmodern openssl \
     && echo "options('repos' = c(CRAN='https://mirrors.tuna.tsinghua.edu.cn/CRAN/'))" >> /home/opencpu/.Rprofile \
     && echo "options(BioC_mirror='https://mirrors.tuna.tsinghua.edu.cn/bioconductor')" >> /home/opencpu/.Rprofile \
+    && Rscript -e "install.packages(c('git2r', 'RCurl'))" \
     && Rscript -e "devtools::install('/tmp/BioInstaller')" \ 
     && Rscript -e "setRepositories(ind=1:2);BioInstaller::check_shiny_dep(TRUE)" \
-    && Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('maftools')" \
+    && runuser -l opencpu -c "export BIO_SOFTWARES_DB_ACTIVE=/home/opencpu/.BioInstaller/info.yaml" \
+    && chown -R opencpu /home/opencpu/ \
+    && echo 'export BIO_SOFTWARES_DB_ACTIVE="~/.BioInstaller/info.yaml"\n' >> /home/opencpu/.bashrc \
+    && echo 'BIO_SOFTWARES_DB_ACTIVE="~/.BioInstaller/info.yaml"\n' >> /home/opencpu/.Renviron \
+    && runuser -l opencpu -c "Rscript -e \"BioInstaller::install.bioinfo('miniconda2', destdir = '/home/opencpu/opt/')\"" \
+    && runuser -l opencpu -c "Rscript -e \"BioInstaller::install.bioinfo('spack', destdir = '/home/opencpu/opt/spack')\"" \
+    && echo 'export PATH=/home/opencpu/opt/miniconda2/bin:$PATH\n' >> /etc/profile \
+    && echo 'export SPACK_ROOT=/home/opencpu/opt/spack;source $SPACK_ROOT/share/spack/setup-env.sh;' >> /etc/profile \
     && echo 'file=`ls /usr/local/lib/R/site-library/`; cd /usr/lib/R/library; for i in ${file}; do rm -rf ${i};done' >> /tmp/rm_script \
     && sh /tmp/rm_script \
     && ln -sf /usr/local/lib/R/site-library/* /usr/lib/R/library/ \
     && rm /tmp/rm_script \
     && rm -rf /tmo/BioInstaller \
     && rm -rf /var/lib/apt/lists/* \
     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+    #&& Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('maftools')" \
 
-CMD service cron start && runuser -l opencpu -c 'export AUTO_CREATE_BIOINSTALLER_DIR="TRUE";Rscript -e "BioInstaller::set_shiny_workers(3, auto_create = TRUE)" &' && runuser -l opencpu -c 'sh /usr/bin/start_shiny_server' && /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND
+CMD service cron start && runuser -s /bin/bash -l opencpu -c '. ~/.bashrc; export AUTO_CREATE_BIOINSTALLER_DIR="TRUE";Rscript -e "BioInstaller::set_shiny_workers(3, auto_create = TRUE)" &' && runuser -s /bin/bash -l opencpu -c '. ~/.bashrc; sh /usr/bin/start_shiny_server' && . /etc/profile; /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND

R/versions.R

@@ -27,7 +27,8 @@ github2versions <- function(github.url) {
     `Accept-Language` = "en-us", Connection = "keep-alive", `Accept-Charset` = "GB2312,utf-8;q=0.7,*;q=0.7")
   url <- sprintf("https://api.github.com/repos/%s/%s/tags?client_id=1d40ab6884d214ef6889&client_secret=23b818c2bad8e9f88dafd8a425613475362b326d", 
     user, repo)
-  txt <- getURL(url, headerfunction = h$update, httpheader = myheader)
+  txt <- tryCatch(getURL(url, headerfunction = h$update, httpheader = myheader), error = function(e) {
+       getURL(url, headerfunction = h$update, httpheader = myheader, ssl.verifypeer = FALSE) })
   json <- tempfile()
   cat(txt, file = json, sep = "\n")
   return(read.config(file = json)$name)

inst/extdata/config/github/github.toml

@@ -689,5 +689,5 @@ github_url = "https://github.com/snakemake-workflows/dna-seq-gatk-variant-callin
 [spack]
 github_url = "https://github.com/spack/spack"
 [spack.install]
-linux = "#R#cat('export SPACK_ROOT={{download.dir}}\nsource $SPACK_ROOT/share/spack/setup-env.sh', file = '~/.bashrc', append = TRUE)#R#"
-mac = "#R#cat('export SPACK_ROOT={{download.dir}}\nsource $SPACK_ROOT/share/spack/setup-env.sh', file = '~/.bashrc', append = TRUE)#R#"
+linux = "#R#cat('export SPACK_ROOT={{download.dir}}\nsource $SPACK_ROOT/share/spack/setup-env.sh;', file = '~/.bashrc', append = TRUE)#R#"
+mac = "#R#cat('export SPACK_ROOT={{download.dir}}\nsource $SPACK_ROOT/share/spack/setup-env.sh;', file = '~/.bashrc', append = TRUE)#R#"

inst/extdata/config/nongithub/nongithub.toml

@@ -612,8 +612,8 @@ linux = ["https://repo.continuum.io/miniconda/Miniconda2-{{version}}-Linux-x86_6
          "http://bioinfo.rjh.com.cn/download/miniconda/Miniconda2-{{version}}-Linux-x86_64.sh"]
 
 [miniconda2.install]
-linux = "sh Miniconda2-{{version}}-Linux-x86_64.sh"
-mac = "sh Miniconda2-{{version}}-MacOSX-x86_64.sh"
+linux = "bash Miniconda2-{{version}}-Linux-x86_64.sh -b -p {{destdir}}/miniconda2 && echo 'export PATH=$HOME/miniconda2/bin:$PATH' >> $HOME/.bashrc"
+mac = "bash Miniconda2-{{version}}-Linux-x86_64.sh -b -p {{destdir}}/miniconda2 && echo 'export PATH=$HOME/miniconda2/bin:$PATH' >> $HOME/.bashrc"
 
 [miniconda3]
 decompress = false
@@ -628,8 +628,8 @@ linux = ["https://repo.continuum.io/miniconda/Miniconda3-{{version}}-Linux-x86_6
          "https://repo.continuum.io/miniconda/Miniconda3-{{version}}-Linux-x86_64.sh"]
 
 [miniconda3.install]
-linux = "sh Miniconda3-{{version}}-Linux-x86_64.sh"
-mac = "sh Miniconda3-{{version}}-MacOSX-x86_64.sh"
+linux = "bash Miniconda3-{{version}}-Linux-x86_64.sh -b -p {{destdir}}/miniconda3 && echo 'export PATH={{destdir}}/miniconda3/bin:$PATH' >> $HOME/.bashrc"
+mac = "bash Miniconda3-{{version}}-Linux-x86_64.sh -b -p {{destdir}}/miniconda3 && echo 'export PATH={{destdir}}/miniconda3/bin:$PATH' >> $HOME/.bashrc"
 
 [strelka]
 source_url = "ftp://[email protected]/v1-branch/v{{version}}/strelka_workflow-{{version}}.tar.gz"

inst/extdata/config/shiny/shiny.spack.parameters.toml

@@ -1,8 +1,9 @@
 [spack.ui.sections]
-order = ["spack_input_box", "spack_output_box_text"]
+order = ["spack_input_box", "spack_output_box_table", "spack_output_box_text"]
 [spack.ui.sections.ui_basic]
 spack_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
-spack_output_box_text = "title = 'Output of spack', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+spack_output_box_text = "title = 'Output of spack (Text)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+spack_output_box_table = "title = 'Output of spack (Table)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 
 [spack.paramters.spack_input_box]
 # For reading annovarR shiny APP spack tool input files  
@@ -29,7 +30,7 @@ spack_sub_cmd = ["list", "info", "find", "install", "uninstall",
                  "view", "create", "edit",
                  "arch", "compilers"]
 [spack.paramters.spack_input_box.input.single_input.selected]
-spack_sub_cmd = "find"
+spack_sub_cmd = "list"
 
 [spack.paramters.spack_input_box.input.start_analysis]
 input_id = "start_spack_analysis"
@@ -43,3 +44,15 @@ render_type = "shiny::renderPrint"
 render_id = "spack_output"
 output_type = "shiny::verbatimTextOutput"
 progressbar_message = "spack ouput"
+
+[spack.paramters.spack_output_box_table]
+section_type = "output"
+rcmd_last = """
+if (spack_sub_cmd == 'list') obj <- as.data.frame(spack.list())
+colnames(obj) <- "item"
+obj
+"""
+render_type = "DT::renderDataTable"
+render_id = "spack_output_table"
+output_type = "DT::dataTableOutput"
+progressbar_message = "spack ouput_box_table"

inst/extdata/shiny/global_var.R

@@ -439,6 +439,6 @@ get_bioinstaller_installed <- function() {
   if (!file.exists(items_db) || file.size (items_db) == 0 || 
       configr::get.config.type (items_db) == FALSE) return(data.frame())
   x <- configr::read.config(items_db)
-  if (is.list(x)) {item_name <- names(x);x <- data.table::rbindlist(x)} else {return(data.frame())}
+  if (is.list(x)) {item_name <- names(x);x <- data.table::rbindlist(x, fill = TRUE)} else {return(data.frame())}
   return(cbind(item_name, x))
 }