Commit 2b73472e authored by mmassaviol's avatar mmassaviol
Browse files

Global update (shiny app, dockerfile)

Shiny app with dowload config file button
Dockerfile with a base from docker hub
parent 1e740e63
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/taxonomy /taxonomy
COPY files /workflow
......@@ -45,12 +8,11 @@ RUN pip3 install cutadapt==2.3
RUN apt-get install -y pigz
RUN Rscript -e 'library("devtools")' \
&& Rscript -e 'devtools::install_github("benjjneb/dada2", ref="v1.12")'
RUN Rscript -e 'library("devtools");devtools::install_github("benjjneb/dada2", ref="v1.12")'
RUN Rscript -e 'devtools::install_github("joey711/phyloseq")'
RUN Rscript -e 'library("devtools");devtools::install_github("joey711/phyloseq")'
RUN Rscript -e 'devtools::install_github("joey711/biomformat")'
RUN Rscript -e 'library("devtools");devtools::install_github("joey711/biomformat")'
RUN cd /opt/biotools \
&& git clone https://github.com/marbl/Krona.git \
......
......@@ -86,12 +86,11 @@ singularity run --app appName this_container.sif
apt-get install -y pigz
Rscript -e 'library("devtools")'
Rscript -e 'devtools::install_github("benjjneb/dada2", ref="v1.12")'
Rscript -e 'library("devtools");devtools::install_github("benjjneb/dada2", ref="v1.12")'
Rscript -e 'devtools::install_github("joey711/phyloseq")'
Rscript -e 'library("devtools");devtools::install_github("joey711/phyloseq")'
Rscript -e 'devtools::install_github("joey711/biomformat")'
Rscript -e 'library("devtools");devtools::install_github("joey711/biomformat")'
cd /opt/biotools
git clone https://github.com/marbl/Krona.git
......
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
......@@ -6,12 +6,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Dada2", tabName="dada2", 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','Trimming'='trimming','Dada2'='dada2',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Trimming'='trimming','Dada2'='dada2')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
......@@ -215,6 +215,13 @@ 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)
......
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/' $fic
RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shiny",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/")'
FROM mmassaviol/mbb_workflows_base:latest
COPY files /workflow
COPY sagApp /sagApp
......
import oyaml as yaml
import shutil
def read_yaml(filepath):
try:
......@@ -15,4 +16,11 @@ def write_yaml(filepath,data):
with open(filepath, 'w') as file:
yaml.dump(data, file, default_flow_style=False)
except IOError as e:
print("Error in file opening:", e)
\ No newline at end of file
print("Error in file opening:", e)
def copy_dir(src,dst):
try:
shutil.copytree(src,dst)
except FileExistsError:
shutil.rmtree(dst, ignore_errors=True)
shutil.copytree(src,dst)
\ No newline at end of file
......@@ -12,12 +12,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Visualize", tabName="visualize", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
menuItem("Rule Graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
tags$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','Trimming'='trimming','Filter'='filter','Assemble'='assemble','Annotate'='annotate','Visualize'='visualize',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Trimming'='trimming','Filter'='filter','Assemble'='assemble','Annotate'='annotate','Visualize'='visualize')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
......@@ -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)
......
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/' $fic
RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shiny",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/")'
FROM mmassaviol/mbb_workflows_base:latest
COPY files /workflow
COPY sagApp /sagApp
......
import oyaml as yaml
import shutil
def read_yaml(filepath):
try:
......@@ -15,4 +16,11 @@ def write_yaml(filepath,data):
with open(filepath, 'w') as file:
yaml.dump(data, file, default_flow_style=False)
except IOError as e:
print("Error in file opening:", e)
\ No newline at end of file
print("Error in file opening:", e)
def copy_dir(src,dst):
try:
shutil.copytree(src,dst)
except FileExistsError:
shutil.rmtree(dst, ignore_errors=True)
shutil.copytree(src,dst)
\ No newline at end of file
......@@ -12,12 +12,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Visualize", tabName="visualize", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
menuItem("Rule Graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
tags$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','Find mitochondrion scaffold'='find_mitoscaf','Annotate'='annotate','Visualize'='visualize',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Quality check'='quality_check','Assembling'='assembling','Find mitochondrion scaffold'='find_mitoscaf','Annotate'='annotate','Visualize'='visualize')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
......@@ -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)
......
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/' $fic
RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shiny",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/")'
FROM mmassaviol/mbb_workflows_base:latest
COPY files /workflow
COPY sagApp /sagApp
......
import oyaml as yaml
import shutil
def read_yaml(filepath):
try:
......@@ -15,4 +16,11 @@ def write_yaml(filepath,data):
with open(filepath, 'w') as file:
yaml.dump(data, file, default_flow_style=False)
except IOError as e:
print("Error in file opening:", e)
\ No newline at end of file
print("Error in file opening:", e)
def copy_dir(src,dst):
try:
shutil.copytree(src,dst)
except FileExistsError:
shutil.rmtree(dst, ignore_errors=True)
shutil.copytree(src,dst)
\ No newline at end of file
......@@ -18,12 +18,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("populations", tabName="populations", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
menuItem("Rule Graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
tags$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','Demultiplexing'='demultiplexing','ustacks'='ustacks','cstacks'='cstacks','sstacks'='stacks','tsv2bam'='tsv2bam','gstacks'='gstacks','populations'='populations',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Quality check'='quality_check','Demultiplexing'='demultiplexing','ustacks'='ustacks','cstacks'='cstacks','sstacks'='stacks','tsv2bam'='tsv2bam','gstacks'='gstacks','populations'='populations')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
......@@ -233,6 +233,13 @@ 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)
......
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/' $fic
RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shiny",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/")'
FROM mmassaviol/mbb_workflows_base:latest
COPY files /workflow
COPY sagApp /sagApp
......
import oyaml as yaml
import shutil
def read_yaml(filepath):
try:
......@@ -15,4 +16,11 @@ def write_yaml(filepath,data):
with open(filepath, 'w') as file:
yaml.dump(data, file, default_flow_style=False)
except IOError as e:
print("Error in file opening:", e)
\ No newline at end of file
print("Error in file opening:", e)
def copy_dir(src,dst):
try:
shutil.copytree(src,dst)
except FileExistsError:
shutil.rmtree(dst, ignore_errors=True)
shutil.copytree(src,dst)
\ No newline at end of file
......@@ -14,12 +14,18 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Populations", tabName="populations", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
menuItem("Rule Graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
tags$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','Demultiplexing'='demultiplexing','Mapping'='mapping','Mapping check'='mapping_check','Gstacks'='gstacks','Populations'='populations',"All"="all")), tags$br(),
selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Quality check'='quality_check','Demultiplexing'='demultiplexing','Mapping'='mapping','Mapping check'='mapping_check','Gstacks'='gstacks','Populations'='populations')), tags$br(),
actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
......
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