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

Update to RMassBank in github main branch #14

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update to RMassBank in github main branch #14

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
16 changes: 5 additions & 11 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,24 +23,18 @@ RUN R -e 'install.packages(c("devtools","readxl","webchem","jsonlite","rcdk","ci
# Install Bioconductor
RUN R CMD javareconf
RUN R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install(ask = FALSE, update = TRUE); BiocManager::install(c("multtest","MSnbase","mzR","MassSpecWavelet","S4Vectors","BiocStyle","faahKO","msdata","xcms","CAMERA"), ask = FALSE, update = TRUE)'
RUN R -e 'library(devtools); devtools::install_github("https://github.com/MassBank/RMassBank", ref="c579455cff45d1971c029a9af9189a9e65429e16")'
#RUN R -e 'library(devtools); devtools::install_github("https://github.com/MassBank/RMassBank", ref="treutler-merge")'
#RUN R -e 'library(devtools); devtools::install_github("https://github.com/MassBank/RMassBank")'
RUN R -e 'library(devtools); install_github(repo = "CDK-R/rinchi@master")'

# Install old version of webchem
RUN R -e 'devtools::install_github("ropensci/webchem")'

# Install RMassBank
WORKDIR /usr/src
RUN git clone https://github.com/MassBank/RMassBank ; cd RMassBank ; git checkout c579455cff45d1971c029a9af9189a9e65429e16
#RUN git clone https://github.com/MassBank/RMassBank
#RUN R -e 'library(devtools); devtools::install_github("https://github.com/MassBank/RMassBank", ref="c579455cff45d1971c029a9af9189a9e65429e16")'
#RUN R -e 'library(devtools); devtools::install_github("https://github.com/MassBank/RMassBank", ref="treutler-merge")'
RUN R -e 'library(devtools); devtools::install_github("https://github.com/MassBank/RMassBank")'

# Install MassBank
#WORKDIR /usr/src
#RUN git clone https://github.com/MassBank/MassBank-web
#WORKDIR /usr/src/MassBank-web/MassBank-Project/
#RUN mvn package
#RUN git clone https://github.com/MassBank/RMassBank ; cd RMassBank ; git checkout c579455cff45d1971c029a9af9189a9e65429e16
#RUN git clone https://github.com/MassBank/RMassBank

# Cleanup
RUN apt-get -y --purge --auto-remove remove make gcc gfortran g++
Expand Down