diff options
Diffstat (limited to 'day2/ex3-R/default.nix')
| -rw-r--r-- | day2/ex3-R/default.nix | 34 |
1 files changed, 23 insertions, 11 deletions
diff --git a/day2/ex3-R/default.nix b/day2/ex3-R/default.nix index 614c24f..7a5d39a 100644 --- a/day2/ex3-R/default.nix +++ b/day2/ex3-R/default.nix @@ -1,9 +1,9 @@ /* This example tries to demonstrate that even very simple workflows (this -is only really one computational stage) can benefit from some formalisation -to provide reproducibility. We borrow part of the edgeR example available from -https://ucdavis-bioinformatics-training.github.io/2018-September-Bioinformatics-Prerequisites/friday/limma_biomart_vignettes.html -and specify it in BioNix so that it's easily reproducible. +is only really one computational stage) can benefit from some +formalisation to provide reproducibility. With help from Hannah Coughlan +the example from Law et al. [1] was adapted and in this exercise we will +fully specify it in BioNix so that it's easily reproducible. One key learning goal in this exercise is to understand that Nix only allows _inputs_ to be referenced during the execution of a build to @@ -12,31 +12,43 @@ forbidden when the build sandbox is enabled (default, but not on Milton for technical reasons), meaning data cannot be fetched as part of a build as the original example does. -We therefore fetch the count input as a separate stage and Nix will take +We therefore fetch the count input as a seperate stage and Nix will take care of downloading it for us. The caveate is that the content of things fetched from the internet must be verified to give reproducibility. Nix does this through hashing. +One important thing to note is this analysis does change depending on +annotation, so achieving reproducibility requires some tooling to fix +the software/database stack. Nix does this for us ensuring +reproducibility. + Goal: fill out the below to specify required R packages, execute the build and observe the hash collision. Update the hash and see if the build now completes successfully. + +Hint: All of CRAN and BioC are available in nixpkgs, however for +convenience periods "." are converted to "_" as "." in the Nix language +is attrset element access. + +1: https://www.bioconductor.org/packages/devel/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html */ {bionix}: with bionix; let R = pkgs.rWrapper.override {packages = with pkgs.rPackages; [];}; - - counts = pkgs.fetchurl { - url = "https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2018-September-Bioinformatics-Prerequisites/master/friday/counts.tsv"; - sha256 = "sha256-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="; - }; in stage { - inherit counts; name = "r-ex"; + src = pkgs.fetchurl { + url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63310&format=file"; + sha256 = "sha256-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="; + }; + buildInputs = [R]; buildCommand = '' + tar xf $src + mkdir $out Rscript ${./script.R} ''; } |