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Change to foreach and doparalle

# 載入所需套件
library(foreach)
library(doParallel)

# 設定要使用的核心數量
num_cores <- 4  # 設定為您希望的核心數量

# 設定 doParallel 參數,並註冊平行處理群集
cl <- makeCluster(num_cores)
registerDoParallel(cl)

# 建立一個迴圈並使用 foreach 進行並行運算
result <- foreach(i = 1:10) %dopar% {
  sqrt(i)
}

# 停止並行處理群集
stopCluster(cl)

# 查看結果
print(result)

Stop all cluster

stopImplicitCluster()

Speed up the Tools

To speed up the EnrichShuf, we could

  1. Use GenomicRanges insteat of ChIPseeker.

Create Anaconda environment

/mnt/nas/joseph/Anaconda3/bin/conda create -n EnrichShuf
## Optional 
/mnt/nas/joseph/Anaconda3/bin/conda init bash

conda activate EnrichShuf
conda install r-essentials r-base==4.2

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
  _r-mutex           pkgs/main/linux-64::_r-mutex-1.0.0-anacondar_1
  _sysroot_linux-64~ pkgs/main/noarch::_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10
  binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.38-h2a08ee3_1
  binutils_linux-64  pkgs/main/linux-64::binutils_linux-64-2.38.0-hc2dff05_0
  blas               pkgs/main/linux-64::blas-1.0-openblas
  bwidget            pkgs/main/linux-64::bwidget-1.9.11-1
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
  c-ares             pkgs/main/linux-64::c-ares-1.18.1-h7f8727e_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.01.10-h06a4308_0
  cairo              pkgs/main/linux-64::cairo-1.16.0-hb05425b_3
  curl               pkgs/main/linux-64::curl-7.88.1-h5eee18b_0
  expat              pkgs/main/linux-64::expat-2.4.9-h6a678d5_0
  fontconfig         pkgs/main/linux-64::fontconfig-2.14.1-h52c9d5c_1
  freetype           pkgs/main/linux-64::freetype-2.12.1-h4a9f257_0
  fribidi            pkgs/main/linux-64::fribidi-1.0.10-h7b6447c_0
  gcc_impl_linux-64  pkgs/main/linux-64::gcc_impl_linux-64-11.2.0-h1234567_1
  gcc_linux-64       pkgs/main/linux-64::gcc_linux-64-11.2.0-h5c386dc_0
  gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-11.2.0-h1234567_1
  gfortran_linux-64  pkgs/main/linux-64::gfortran_linux-64-11.2.0-hc2dff05_0
  glib               pkgs/main/linux-64::glib-2.69.1-he621ea3_2
  graphite2          pkgs/main/linux-64::graphite2-1.3.14-h295c915_1
  gxx_impl_linux-64  pkgs/main/linux-64::gxx_impl_linux-64-11.2.0-h1234567_1
  gxx_linux-64       pkgs/main/linux-64::gxx_linux-64-11.2.0-hc2dff05_0
  harfbuzz           pkgs/main/linux-64::harfbuzz-4.3.0-hd55b92a_0
  icu                pkgs/main/linux-64::icu-58.2-he6710b0_3
  jpeg               pkgs/main/linux-64::jpeg-9e-h5eee18b_1
  kernel-headers_li~ pkgs/main/noarch::kernel-headers_linux-64-3.10.0-h57e8cba_10
  krb5               pkgs/main/linux-64::krb5-1.19.4-h568e23c_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  lerc               pkgs/main/linux-64::lerc-3.0-h295c915_0
  libcurl            pkgs/main/linux-64::libcurl-7.88.1-h91b91d3_0
  libdeflate         pkgs/main/linux-64::libdeflate-1.17-h5eee18b_0
  libedit            pkgs/main/linux-64::libedit-3.1.20221030-h5eee18b_0
  libev              pkgs/main/linux-64::libev-4.33-h7f8727e_1
  libffi             pkgs/main/linux-64::libffi-3.4.2-h6a678d5_6
  libgcc-devel_linu~ pkgs/main/linux-64::libgcc-devel_linux-64-11.2.0-h1234567_1
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1
  libgfortran5       pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
  libnghttp2         pkgs/main/linux-64::libnghttp2-1.46.0-hce63b2e_0
  libopenblas        pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0
  libpng             pkgs/main/linux-64::libpng-1.6.39-h5eee18b_0
  libssh2            pkgs/main/linux-64::libssh2-1.10.0-h8f2d780_0
  libstdcxx-devel_l~ pkgs/main/linux-64::libstdcxx-devel_linux-64-11.2.0-h1234567_1
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
  libtiff            pkgs/main/linux-64::libtiff-4.5.0-h6a678d5_2
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
  libwebp-base       pkgs/main/linux-64::libwebp-base-1.2.4-h5eee18b_1
  libxcb             pkgs/main/linux-64::libxcb-1.15-h7f8727e_0
  libxml2            pkgs/main/linux-64::libxml2-2.9.14-h74e7548_0
  lz4-c              pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_0
  make               pkgs/main/linux-64::make-4.2.1-h1bed415_1
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
  openssl            pkgs/main/linux-64::openssl-1.1.1t-h7f8727e_0
  pango              pkgs/main/linux-64::pango-1.50.7-h05da053_0
  pcre               pkgs/main/linux-64::pcre-8.45-h295c915_0
  pcre2              pkgs/main/linux-64::pcre2-10.37-he7ceb23_1
  pixman             pkgs/main/linux-64::pixman-0.40.0-h7f8727e_1
  r-base             pkgs/r/linux-64::r-base-4.2.0-h1ae530e_0
  r-essentials       pkgs/r/linux-64::r-essentials-0.1.0-r42h76d94ec_0
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0
  sysroot_linux-64   pkgs/main/noarch::sysroot_linux-64-2.17-h57e8cba_10
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
  tktable            pkgs/main/linux-64::tktable-2.10-h14c3975_0
  xz                 pkgs/main/linux-64::xz-5.2.10-h5eee18b_1
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
  zstd               pkgs/main/linux-64::zstd-1.5.2-ha4553b6_0

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