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Commit 2b73472e authored by mmassaviol's avatar mmassaviol
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Global update (shiny app, dockerfile) 

Shiny app with dowload config file button
Dockerfile with a base from docker hub
parent 1e740e63
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Inline Side-by-side
RADseq_ref/sagApp/app.R
View file @ 2b73472e
......@@ -227,6 +227,13 @@ observeEvent(input$unlock,{
input_list <- reactiveValuesToList(input)
toggle_inputs(input_list,T,F)
})
output$DownloadParams <- downloadHandler(
filename = function() {
paste0("params", Sys.Date(), ".yaml", sep="")
},
content = function(file) {
save_params(file)
})
source("./server/opt_global.R", local=T)
......
Variant_calling/Dockerfile
View file @ 2b73472e
FROM rocker/r-ver:3.5.3
ENV PATH /opt/biotools/bin:$PATH
ENV ROOTSYS /opt/biotools/root
ENV LD_LIBRARY_PATH '$LD_LIBRARY_PATH:$ROOTSYS/lib'
RUN apt-get update
RUN apt-get install -yq tzdata
RUN apt-get install -y locales
RUN locale-gen "en_US.UTF-8"
RUN export LC_ALL=en_US.UTF-8
RUN export LANG=en_US.UTF-8
RUN apt-get install -y curl wget apt-utils
RUN apt-get install -y gcc fort77 aptitude
RUN aptitude install -y g++ xorg-dev libreadline-dev gfortran
RUN apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev liblapack3 git nano graphviz python3 python3-pip
RUN apt-get install -y autotools-dev automake cmake grep sed dpkg fuse zip build-essential pkg-config bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev
RUN apt-get clean
RUN if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
RUN if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi
RUN chmod 777 -R /opt/biotools/
ENV PATH /opt/biotools/bin:$PATH
RUN pip3 install snakemake==5.4.0 oyaml
RUN pip3 install multiqc==1.7
RUN fic=$(find /usr/ -name stacks.py) && sed -i 's/out_dict\[s_name\] = cdict/out_dict\[content\[0\]\] = cdict/' $fic
RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shiny",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/")'
FROM mmassaviol/mbb_workflows_base:latest
COPY files /workflow
COPY sagApp /sagApp
......
Variant_calling/files/scripts/.gitignore 0 → 100644
View file @ 2b73472e
# Ignore everything in this directory
*
# Except this file
!.gitignore
Variant_calling/files/tools.py
View file @ 2b73472e
import oyaml as yaml
import shutil
def read_yaml(filepath):
try:
......@@ -15,4 +16,11 @@ def write_yaml(filepath,data):
with open(filepath, 'w') as file:
yaml.dump(data, file, default_flow_style=False)
except IOError as e:
print("Error in file opening:", e)
\ No newline at end of file
print("Error in file opening:", e)
def copy_dir(src,dst):
try:
shutil.copytree(src,dst)
except FileExistsError:
shutil.rmtree(dst, ignore_errors=True)
shutil.copytree(src,dst)
\ No newline at end of file
Variant_calling/sagApp/R/menugauche.R
View file @ 2b73472e
......@@ -12,12 +12,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Variant calling", tabName="variant_calling", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
menuItem("Rule Graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
tags$br(),
downloadButton("DownloadParams", "Download config file", class="btn btn-light", style="color:black;margin: 6px 5px 6px 15px;"),
tags$br(),
tags$br(),
numericInput("cores", label = "Threads available", min = 1, max = 24, step = 1, width = "auto", value = 16),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('none'='none','Preprocessing'='preprocess','Mapping'='mapping','Mark Duplicates'='mark_duplicates','Indel Realign'='indel_realign','Variant calling'='variant_calling',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Preprocessing'='preprocess','Mapping'='mapping','Mark Duplicates'='mark_duplicates','Indel Realign'='indel_realign','Variant calling'='variant_calling')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
Variant_calling/sagApp/app.R
View file @ 2b73472e
......@@ -224,6 +224,13 @@ observeEvent(input$unlock,{
input_list <- reactiveValuesToList(input)
toggle_inputs(input_list,T,F)
})
output$DownloadParams <- downloadHandler(
filename = function() {
paste0("params", Sys.Date(), ".yaml", sep="")
},
content = function(file) {
save_params(file)
})
source("./server/opt_global.R", local=T)
......
Virus_Assembler_Megahit/Dockerfile
View file @ 2b73472e
FROM rocker/r-ver:3.5.3
ENV PATH /opt/biotools/bin:$PATH
ENV ROOTSYS /opt/biotools/root
ENV LD_LIBRARY_PATH '$LD_LIBRARY_PATH:$ROOTSYS/lib'
RUN apt-get update
RUN apt-get install -yq tzdata
RUN apt-get install -y locales
RUN locale-gen "en_US.UTF-8"
RUN export LC_ALL=en_US.UTF-8
RUN export LANG=en_US.UTF-8
RUN apt-get install -y curl wget apt-utils
RUN apt-get install -y gcc fort77 aptitude
RUN aptitude install -y g++ xorg-dev libreadline-dev gfortran
RUN apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev liblapack3 git nano graphviz python3 python3-pip
RUN apt-get install -y autotools-dev automake cmake grep sed dpkg fuse zip build-essential pkg-config bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev
RUN apt-get clean
RUN if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
RUN if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi
RUN chmod 777 -R /opt/biotools/
ENV PATH /opt/biotools/bin:$PATH
RUN pip3 install snakemake==5.4.0 oyaml
RUN pip3 install multiqc==1.7
RUN fic=$(find /usr/ -name stacks.py) && sed -i 's/out_dict\[s_name\] = cdict/out_dict\[content\[0\]\] = cdict/' $fic
RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shiny",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/")'
FROM mmassaviol/mbb_workflows_base:latest
COPY ./files/data/blast_db_virus /blast_db_virus
COPY files /workflow
......
Virus_Assembler_Megahit/files/scripts/.gitignore 0 → 100644
View file @ 2b73472e
# Ignore everything in this directory
*
# Except this file
!.gitignore
Virus_Assembler_Megahit/files/tools.py
View file @ 2b73472e
import oyaml as yaml
import shutil
def read_yaml(filepath):
try:
......@@ -15,4 +16,11 @@ def write_yaml(filepath,data):
with open(filepath, 'w') as file:
yaml.dump(data, file, default_flow_style=False)
except IOError as e:
print("Error in file opening:", e)
\ No newline at end of file
print("Error in file opening:", e)
def copy_dir(src,dst):
try:
shutil.copytree(src,dst)
except FileExistsError:
shutil.rmtree(dst, ignore_errors=True)
shutil.copytree(src,dst)
\ No newline at end of file
Virus_Assembler_Megahit/sagApp/R/menugauche.R
View file @ 2b73472e
......@@ -10,12 +10,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Mapping", tabName="mapping", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
menuItem("Rule Graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
tags$br(),
downloadButton("DownloadParams", "Download config file", class="btn btn-light", style="color:black;margin: 6px 5px 6px 15px;"),
tags$br(),
tags$br(),
numericInput("cores", label = "Threads available", min = 1, max = 24, step = 1, width = "auto", value = 16),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('none'='none','Quality check'='quality_check','Assembling'='assembling','Blasting'='blasting','Mapping'='mapping',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Quality check'='quality_check','Assembling'='assembling','Blasting'='blasting','Mapping'='mapping')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
Virus_Assembler_Megahit/sagApp/app.R
View file @ 2b73472e
......@@ -221,6 +221,13 @@ observeEvent(input$unlock,{
input_list <- reactiveValuesToList(input)
toggle_inputs(input_list,T,F)
})
output$DownloadParams <- downloadHandler(
filename = function() {
paste0("params", Sys.Date(), ".yaml", sep="")
},
content = function(file) {
save_params(file)
})
source("./server/opt_global.R", local=T)
......
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