diff options
| author | pjotr | 2026-05-31 09:25:31 +0000 |
|---|---|---|
| committer | pjotr | 2026-05-31 09:25:31 +0000 |
| commit | 70cf276c980ce66f14076196cdba5db6f482bea1 (patch) | |
| tree | 4ea6a51ee27a6bd96edff10fa4154be8c29c5cf0 | |
| parent | fd32c0ab2acefbe8e0304ec6623650b95d960adc (diff) | |
| download | guix-bioinformatics-70cf276c980ce66f14076196cdba5db6f482bea1.tar.gz | |
Propagate tools in gemma-wrapper
| -rw-r--r-- | gn/packages/gemma.scm | 11 |
1 files changed, 9 insertions, 2 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm index ce486e6..9b44759 100644 --- a/gn/packages/gemma.scm +++ b/gn/packages/gemma.scm @@ -19,6 +19,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages parallel) #:use-module (gnu packages perl) + #:use-module (gnu packages textutils) #:use-module (gnu packages time) #:use-module (gnu packages web) #:use-module (gnu packages ruby-check) @@ -140,8 +141,14 @@ genome-wide association studies (GWAS).") (native-inputs (list ruby-rake)) (inputs (list gemma-gn2)) (propagated-inputs - (list parallel ;; bin/gemma-wrapper shells out to GNU parallel - coreutils)) ;; uses cat + ;; bin/gemma-wrapper shells out to all of these; propagate + ;; them so `guix shell gemma-wrapper` is a complete runtime. + (list parallel ;; orchestrates per-chromosome and permutation jobs + coreutils ;; uses cat, env, rm + tar ;; archives GEMMA's per-run outputs as .tar.xz + xz ;; tar -J needs xz on PATH + time ;; bin/gemma-wrapper invokes `time -v gemma ...` + pfff)) ;; fast file fingerprint for inputs >100KB (arguments (list #:phases |