Last updated: 2019-10-01
Checks: 7 0
Knit directory: listerlab/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e65ab6f | davetang | 2019-10-01 | wflow_publish(files = c(“analysis/machete.Rmd”, “analysis/index.Rmd”)) |
| html | 21e7535 | davetang | 2019-10-01 | Build site. |
| Rmd | 31e33bb | davetang | 2019-10-01 | wflow_publish(files = c(“analysis/machete.Rmd”, “analysis/stiletto.Rmd”)) |
| html | 31e33bb | davetang | 2019-10-01 | wflow_publish(files = c(“analysis/machete.Rmd”, “analysis/stiletto.Rmd”)) |
R compiled in /opt/R. The following packages were installed using YUM so that we could compile R.
sudo yum install readline-devel
sudo yum install libXt-devel
sudo yum install zlib-devel
sudo yum install bzip2-devel
sudo yum install xz xz-devel
sudo yum install pcre-devel
sudo yum install libcurl-devel
sudo yum reinstall libcurl curl libcurl-devel
sudo yum install cairo-devel pango-devel libpng-devel
sudo yum install openssl-devel
sudo yum install java-1.8.0-openjdk-develThe source code for the latest version of R (as of 2018/10/11) was downloaded and compiled.
wget -c -N https://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
tar -xzf R-3.5.1.tar.gz
sudo mkdir -p /opt/R/3.5.1
cd R-3.5.1.tar.gz
./configure --prefix=/opt/R/3.5.1 --with-x=yes --enable-R-shlib=yes --with-cairo=yes --with-libpng=yes
make
sudo make installR is installed in /opt/R/3.5.1/bin/, so either add this to your PATH or add a symlink to the binary in a directory that is included in your PATH.
I would recommend using one of the working directories for keeping your R packages. Create a .Rprofile file in your home directory and add this line in the file. If the directory doesn’t exist, create it first; substitute dtang with your username.
mkdir -p /home/dtang/working_data_04/R/packages
# add this line in your .Rprofile file
.libPaths("/home/dtang/working_data_04/R/packages/")To install Seurat, first install the R package hdf5r. I downloaded the latest HDF5 binaries and placed them into /opt/hdf5/; note that this directory is not included in PATH by default. Once downloaded, I ran sudo ./h5redeploy to rebuild the paths. Finally, symlinks to libhdf5_hl.so.100 and libhdf5.so.101 were placed in /usr/local/lib64.
The following steps were performed to to install Seurat.
install.packages("devtools")
my_path <- paste0("/opt/hdf5/latest/bin:", Sys.getenv("PATH"))
Sys.setenv(PATH = my_path)
my_lib_path <- paste0("/opt/hdf5/latest/lib:", Sys.getenv("LD_LIBRARY_PATH"))
Sys.setenv(LD_LIBRARY_PATH = my_lib_path)
devtools::install_github(repo = "hhoeflin/hdf5r")
install.packages("Seurat", Ncpus = 16)https://github.com/guoweilong/cgmaptools
cd /opt/
sudo git clone https://github.com/guoweilong/cgmaptools.git && cd cgmaptools
sudo ./install.shPlease add the following line to your ~/.bash_profile, and source ~/.bash_profile before running cgmaptools.
export PATH=/opt/cgmaptools:$PATH
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 purrr_0.3.2
[5] readr_1.3.1 tidyr_0.8.3 tibble_2.1.3 ggplot2_3.2.1
[9] tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 cellranger_1.1.0 pillar_1.4.2 compiler_3.6.1
[5] git2r_0.26.1 workflowr_1.4.0 tools_3.6.1 zeallot_0.1.0
[9] digest_0.6.20 lubridate_1.7.4 jsonlite_1.6 evaluate_0.14
[13] nlme_3.1-141 gtable_0.3.0 lattice_0.20-38 pkgconfig_2.0.2
[17] rlang_0.4.0 cli_1.1.0 rstudioapi_0.10 yaml_2.2.0
[21] haven_2.1.1 xfun_0.9 withr_2.1.2 xml2_1.2.2
[25] httr_1.4.1 knitr_1.24 vctrs_0.2.0 hms_0.5.1
[29] generics_0.0.2 fs_1.3.1 rprojroot_1.3-2 grid_3.6.1
[33] tidyselect_0.2.5 glue_1.3.1 R6_2.4.0 readxl_1.3.1
[37] rmarkdown_1.15 modelr_0.1.5 magrittr_1.5 whisker_0.4
[41] backports_1.1.4 scales_1.0.0 htmltools_0.3.6 rvest_0.3.4
[45] assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3 lazyeval_0.2.2
[49] munsell_0.5.0 broom_0.5.2 crayon_1.3.4