Last updated: 2019-10-24

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Knit directory: listerlab/

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Rmd 235ab5e davetang 2019-10-24 wflow_publish(files = c(“analysis/index.Rmd”, “analysis/bcl2fastq.Rmd”))

bcl2fastq is required for Cell Ranger but is not included in the package. This short guide provides instructions for compiling bcl2fastq on the Pawsey systems (but should work for stiletto too). First download the source code and extract.

wget ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2-20-0-tar.zip

unzip bcl2fastq2-v2-20-0-tar.zip
tar -xzf bcl2fastq2-v2.20.0.422-Source.tar.gz

Create a build directory and go into the extracted directory.

mkdir bcl2fastq2-v2.20.0.422-build

cd bcl2fastq

Use your favourite text editor and create a file (e.g. make.sh) with the following, where

  • TMP should be the directory where you downloaded bcl2fastq2-v2-20-0-tar.zip
  • SOURCE should be the same
  • BUILD should be the same
  • INSTALL_DIR should be set to the directory where you want bcl2fastq installed
#!/bin/bash

export TMP=/home/dtang/group/software/tmp
export SOURCE=${TMP}/bcl2fastq
export BUILD=${TMP}/bcl2fastq2-v2.20.0.422-build
export INSTALL_DIR=/home/dtang/bin

mkdir ${BUILD}
cd ${BUILD}
${SOURCE}/src/configure --prefix=${INSTALL_DIR}

make
make install

Finally, make the file executable and run.

# you should be in the bcl2fastq directory
chmod 755 make.sh
./make.sh

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_1.0.0     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_0.6.21    lubridate_1.7.4  jsonlite_1.6     evaluate_0.14   
[13] lifecycle_0.1.0  nlme_3.1-141     gtable_0.3.0     lattice_0.20-38 
[17] pkgconfig_2.0.3  rlang_0.4.0      cli_1.1.0        rstudioapi_0.10 
[21] yaml_2.2.0       haven_2.1.1      xfun_0.10        withr_2.1.2     
[25] xml2_1.2.2       httr_1.4.1       knitr_1.25       hms_0.5.1       
[29] generics_0.0.2   fs_1.3.1         vctrs_0.2.0      rprojroot_1.3-2 
[33] grid_3.6.1       tidyselect_0.2.5 glue_1.3.1       R6_2.4.0        
[37] readxl_1.3.1     rmarkdown_1.16   modelr_0.1.5     magrittr_1.5    
[41] whisker_0.4      backports_1.1.5  scales_1.0.0     htmltools_0.4.0 
[45] rvest_0.3.4      assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3   
[49] lazyeval_0.2.2   munsell_0.5.0    broom_0.5.2      crayon_1.3.4