diff options
Diffstat (limited to 'scripts/precompute')
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 6 | ||||
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 21 |
2 files changed, 19 insertions, 8 deletions
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index a18b33d..203dfbb 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -1,8 +1,8 @@ #! 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. +This is the *obsolete* script to compute GEMMA directly from the DB. We have split out +this step into separate steps for (1) fetching traits and (2) running gemma without DB. +This allows scaling up on HPC etc. Run from base dir with diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index b14927a..36edf8b 100755 --- a/scripts/precompute/run-gemma.scm +++ b/scripts/precompute/run-gemma.scm @@ -5,9 +5,9 @@ GEMMA on those. Run from base dir with -guix shell guile guile-dbi -- guile -L ../.. -s run-gemma.scm --help + ~/opt/guix-pull/bin/guix shell guile guile-dbi guile-json -- guile -L . -e main -s scripts/precompute/run-gemma.scm 115476.json -and with some extra paths +and with some extra paths (for gemma) . .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 @@ -33,10 +33,21 @@ and with some extra paths (help (single-char #\h) (value #f)))) (options (getopt-long args option-spec)) (help-wanted (option-ref options 'help #f))] + (display "RUNNING") (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") -))) +")) + (let [(trait-name "115475")] + (call-with-input-file "115475.json" + (lambda (port) + (let* [(json (json->scm port)) + (dataset (assoc-ref json "traits")) + (dataset-name (car (car dataset))) + (traits (assoc-ref dataset dataset-name)) + ] + (display dataset) + (write-pheno-file "pheno.txt" traits) + ; (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits))) + )))))) |