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conda
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On project area(19-06-2020)
module load Anaconda2/2019.03
source /cluster/software/Anaconda2/2019.03/etc/profile.d/conda.sh
conda create -y -c conda-forge -c bioconda java-jdk r-essentials=3.6.0 --prefix=/cluster/projects/nn9736k/conda/R-3.6.0
conda activate /cluster/projects/nn9736k/conda/R-3.6.0
conda install -y -c conda-forge -c r r-devtools r-zip=2.0.4 r-openxlsx=4.1.4 r-mclust=5.4.6 r-doParallel=1.0.15 r-chron=2.3-55 r-BH=1.72.0-3
export LD_LIBRARY_PATH=/cluster/projects/nn9736k/conda/R-3.6.0/lib:$LD_LIBRARY_PATH
Install dplyr 0.8.4
> remove.packages("dplyr")
> packageVersion("dplyr")
> library(devtools)
> install.packages("plogr", repo="cran.uib.no")
> packageurl <- "https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.4.tar.gz"
> install.packages(packageurl, repos=NULL, type="source")
----
conda env create --prefix /cluster/work/support/sabryr/conda/pmetrics/R-3.5.1.2 -f environment.yml
ln -s x86_64-conda_cos6-linux-gnu-gcc gcc
ln -s x86_64-conda_cos6-linux-gnu-gfortran gfortran
-----
conda create -y -c r -c conda-forge -c bioconda libgfortran gfortran_linux-64 java-jdk r-base==3.5.1 \
r-xtable r-rjson r-utf8 r-openxlsx r-mgcv r-devtools r-httpuv=1.5.2 r-shiny \
--prefix=/cluster/work/support/sabryr/conda/pmetrics/R-3.5.1.1
conda activate /cluster/work/support/sabryr/conda/pmetrics/R-3.5.1.1
conda install -y -c conda-forge r-openssl=1.4.1 r-curl=4.3 r-jsonlite=1.6.1
----
gcc R-3.6.0
module load Anaconda2/2019.03
source /cluster/software/Anaconda2/2019.03/etc/profile.d/conda.sh
conda create -y -c conda-forge -c bioconda java-jdk r-essentials=3.6.0 \
--prefix=/cluster/work/support/sabryr/conda/pmetrics/R-3.6.0
conda activate /cluster/work/support/sabryr/conda/pmetrics/R-3.6.0
conda install -y -c conda-forge -c r r-devtools r-zip=2.0.4 r-openxlsx=4.1.4 r-mclust=5.4.6 r-doParallel=1.0.15 r-chron=2.3-55 r-BH=1.72.0-3
export LD_LIBRARY_PATH=/cluster/work/support/sabryr/conda/pmetrics/R-3.6.0/lib:$LD_LIBRARY_PATH
-----
gcc 5.3
gfortran_linux-64 5.4.0
conda create -y -c r -c conda-forge -c bioconda libgfortran==5.4.0 gfortran_linux-64==5.4.0 java-jdk r-base==3.5.1 \
r-xtable r-rjson r-utf8 r-openxlsx r-mgcv r-devtools r-httpuv=1.5.2 r-shiny \
--prefix=/cluster/work/support/sabryr/conda/pmetrics/libgfortran5.4.0
conda activate /cluster/work/support/sabryr/conda/pmetrics/libgfortran5.4.0
conda install -y -c conda-forge r-openssl=1.4.1 r-curl=4.3 r-jsonlite=1.6.1
# Find all libraris
for file in $(find -name DESCRIPTION); do grep "Package:\|Version" $file; done;
wget http://www.lapk.org/software/Pmetrics/Examples.zip
For saga.sigma2.no using conda
1. login to saga.sigma2.no
2. https://github.uio.no/sabryr/Pmetrics_test.git
3. cd Pmetrics_test
4. module load Anaconda2/2019.03
5. conda create -y -c r -c conda-forge -c bioconda gcc r-base==3.6.0 r-xtable java-jdk --prefix=/cluster/work/support/sabryr/conda/pmetrics/1.5.2.1
6. conda install -y -c r -c psi4 gcc-5 r-rjson r-utf8 r-openxlsx
7. source /cluster/software/Anaconda2/2019.03/etc/profile.d/conda.sh
8. conda activate /cluster/work/support/sabryr/conda/pmetrics/1.5.2.1
9. export LD_LIBRARY_PATH=/cluster/work/support/sabryr/conda/pmetrics/1.5.2.1/lib
-----------------------------------------------
source /cluster/work/support/Anaconda3/setup.source
#conda create -y -c r -c conda-forge -c bioconda libgfortran gfortran_linux-64 java-jdk r-base==3.5.1 r-xtable r-rjson r-utf8 r-openxlsx r-mgcv --prefix=/cluster/work/support/sabryr/conda/pmetrics/R3.5.1
conda create -y -c r -c conda-forge -c bioconda libgfortran gfortran_linux-64 java-jdk r-base==3.5.1 r-xtable r-rjson r-utf8 r-openxlsx r-mgcv --prefix=/cluster/work/support/sabryr/conda/pmetrics/R-3.5.1
#conda install -y -c r r-rjson r-utf8 r-openxlsx r-mgcv
conda activate /cluster/work/support/sabryr/conda/pmetrics/R-3.5.1
export R_LIBS=/cluster/projects/nn9997k/sabryr/Pmetrics_test/R
export LD_LIBRARY_PATH=/cluster/work/support/sabryr/conda/pmetrics/1.5.2.1/lib
echo "#export R_LIBS=" > rpackages.list
echo "myrepo=\"http://cran.r-project.org\"" >> rpackages.list
awk -F "r-" '{print $NF}' requirements.txt | awk -F "==" '{print "install.packages(\""$1"\", version=\""$2"\", repos=myrepo)"}' >> rpackages.list