Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fixed the docker build #24

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
Open

Fixed the docker build #24

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9b3c49e
fixed apt-get bug working on tidyverse bug
Milldrew Jul 10, 2023
24d8f99
recommended Docker file update - tested on mac build
neodei Jul 11, 2023
ae28344
Merge pull request #1 from AdvaitaBioDevelopers/2.2.2
neodei Jul 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
36 changes: 33 additions & 3 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,17 @@ WORKDIR /app
COPY www /app/www
COPY R /app/R

RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean
RUN apt-get update --allow-releaseinfo-change && apt-get upgrade -y && apt-get clean
RUN apt-get remove -y binutils && apt-get clean
RUN apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean
RUN apt-get install -y libcurl4-openssl-dev unixodbc-dev && apt-get clean
RUN apt-get install -y gfortran
RUN apt-get update && apt-get clean
RUN apt-get update --allow-releaseinfo-change && apt-get clean
RUN apt-get install -y libhdf5-dev
RUN apt-get -y install libcairo2-dev libxt-dev libfontconfig1-dev
# support libraries added tested with buld on mac, addresses tidyverse build issue, fftw3 added for "metap"
RUN apt-get install -y build-essential
RUN apt-get install -y libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
RUN apt-get install -y libgsl-dev
RUN apt-get update && apt-get clean


Expand All @@ -27,6 +32,8 @@ RUN R -e 'library(BiocManager)'
RUN R -e 'install.packages("tidyverse", dep = T)'
RUN R -e 'library(tidyverse)'
# seurat
# * added gfortran overide to build-essential for newer package - tidyverse uses the older version
RUN apt-get install -y gfortran
RUN R -e 'install.packages("Seurat", dep = T)'
RUN R -e 'library(Seurat)'
RUN R -e 'install.packages("SeuratObject", dep = T)'
Expand Down Expand Up @@ -133,3 +140,26 @@ RUN chmod a+rwx -R /app
# Init image
CMD ./init_app.sh

# The error is caused by the fact that the 'tidyverse' package is not installed in the system. You can fix it by modifying the Dockerfile to include the installation of the 'tidyverse' package before calling the 'library' function. Here is an updated version of the Dockerfile:
#
# ```
# FROM rocker/tidyverse:latest
#
# # install dependencies
# RUN apt-get update && apt-get install -y git-core libssl-dev libcurl4-gnutls-dev
#
# # install packages
# RUN R -e 'install.packages(c("tidyverse", "Seurat"), dependencies = TRUE)'
#
# # set working directory
# WORKDIR /app
#
# # copy files
# COPY . /app
#
# # run analysis
# CMD ["Rscript", "analysis.R"]
# ```
#
# Note that we have added the installation of the 'tidyverse' package, along with the 'Seurat' package, using the same R command. This should fix the issue and allow you to run the Docker container without errors.
#