diff options
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 8 | ||||
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 42 |
2 files changed, 49 insertions, 1 deletions
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 8f27bbe..a18b33d 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -1,4 +1,10 @@ -#! Run from base dir with +#! Precompute hits + +This is the obsolete script to compute GEMMA directly from the DB. We have split out +this step into fetching traits and running gemma without DB. This allows scaling up +on HPC etc. + +Run from base dir with . .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm new file mode 100755 index 0000000..b14927a --- /dev/null +++ b/scripts/precompute/run-gemma.scm @@ -0,0 +1,42 @@ +#! Run GEMMA + +A simple script that takes the JSON input from list-traits-to-compute and runs +GEMMA on those. + +Run from base dir with + +guix shell guile guile-dbi -- guile -L ../.. -s run-gemma.scm --help + +and with some extra paths + +. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/run-gemma.scm + +!# + +(use-modules ; (gn data dataset) + ; (gn data hits) + ; (gn data strains) + ; (gn util convert) + (gn runner gemma) + (ice-9 getopt-long) + (ice-9 match) + (ice-9 textual-ports) + (json) + (rnrs bytevectors) + (srfi srfi-1) + ) + +(define (main args) + ;; (write args) + (let* [ + (option-spec '( (version (single-char #\v) (value #f)) + (help (single-char #\h) (value #f)))) + (options (getopt-long args option-spec)) + (help-wanted (option-ref options 'help #f))] + (if help-wanted + (format #t "list-traits-to-compute writes JSON traits files from the GN DB +Usage: list-traits-to-compute [options...] + -h, --help Display this help +") + (display "gemma-run") +))) |