diff options
Diffstat (limited to '.guix/hsmice-test.scm')
| -rw-r--r-- | .guix/hsmice-test.scm | 209 |
1 files changed, 131 insertions, 78 deletions
diff --git a/.guix/hsmice-test.scm b/.guix/hsmice-test.scm index ee8ecbd..1982f65 100644 --- a/.guix/hsmice-test.scm +++ b/.guix/hsmice-test.scm @@ -49,7 +49,7 @@ (define-public r-mixed-model-gwas (package (name "r-mixed-model-gwas") - (version "1.3") + (version "1.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -58,7 +58,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0yv86mw9m981vzl80j100lg05kc6jm5ijhq9b8zcd8f2lr3115db")))) + "0vll55v8wjc0179n5q9ch9ah3dvgymc374wlbz33yzyi35yr8ds2")))) (build-system r-build-system) (home-page "https://github.com/encryption4genetics/mixed-model-gwas") (synopsis "R mixed model GWAS") @@ -66,83 +66,136 @@ genome-wide association study} library for R.") (license license:gpl3+))) -(define test-profile - (profile - (content (packages->manifest (list gzip tar pyhegp - python python-click python-pandas - r r-dplyr r-genio - r-mixed-model-gwas r-purrr - r-qqman r-readr r-stringr - r-tibble r-tidyr))))) - -(define wrangle-script - (local-file "../e2e-tests/hsmice/wrangle.r")) - -(define gwas-script - (local-file "../e2e-tests/hsmice/gwas.r")) - -(define check-qtl-script - (local-file "../e2e-tests/hsmice/check-qtl.py")) - -(define hsmice-test-gexp - (with-imported-modules '((guix build utils)) - #~(begin - (use-modules (guix build utils)) - - (mkdir #$output) - (set-path-environment-variable - "PATH" '("/bin") '(#$test-profile)) - (set-path-environment-variable - "GUIX_PYTHONPATH" - '(#$(string-append "/lib/python" - (version-major+minor (package-version python)) - "/site-packages")) - '(#$test-profile)) - (set-path-environment-variable - "R_LIBS_SITE" '("/site-library") '(#$test-profile)) - (invoke "tar" "-xvf" #$hsmice-data - "./HSmice/1_QTL_data/") - (invoke "Rscript" #$wrangle-script "HSmice/1_QTL_data" ".") - - ;; GWAS on plaintext - (invoke "Rscript" #$gwas-script - "genotype.tsv" "phenotype.tsv" - (string-append #$output "/plaintext-pvalues")) - (copy-file "Rplots.pdf" (string-append #$output "/plaintext-manhattan.pdf")) - - ;; GWAS with simple ciphertext data sharing - (invoke "pyhegp" "encrypt" "genotype.tsv" "phenotype.tsv") - (invoke "Rscript" #$gwas-script - "genotype.tsv.hegp" "phenotype.tsv.hegp" - (string-append #$output "/ciphertext-pvalues")) - (copy-file "Rplots.pdf" - (string-append #$output "/ciphertext-manhattan.pdf")) - - ;; Joint federated GWAS - (invoke "pyhegp" "summary" "genotype1.tsv" "-o" "summary1") - (invoke "pyhegp" "summary" "genotype2.tsv" "-o" "summary2") - (invoke "pyhegp" "pool" "-o" "complete-summary" "summary1" "summary2") - (invoke "pyhegp" "encrypt" "-s" "complete-summary" "genotype1.tsv" "phenotype1.tsv") - (invoke "pyhegp" "encrypt" "-s" "complete-summary" "genotype2.tsv" "phenotype2.tsv") - (invoke "pyhegp" "cat-genotype" "-o" "complete-genotype.tsv.hegp" - "genotype1.tsv.hegp" "genotype2.tsv.hegp") - (invoke "pyhegp" "cat-phenotype" "-o" "complete-phenotype.tsv.hegp" - "phenotype1.tsv.hegp" "phenotype2.tsv.hegp") - (invoke "Rscript" #$gwas-script - "complete-genotype.tsv.hegp" "complete-phenotype.tsv.hegp" - (string-append #$output "/federated-ciphertext-pvalues")) - (copy-file "Rplots.pdf" - (string-append #$output "/federated-ciphertext-manhattan.pdf")) - - ;; Check that the QTL is where it should be. - (for-each (lambda (pvalues-file) - (invoke "python3" #$check-qtl-script - (string-append #$output "/" pvalues-file))) - (list "plaintext-pvalues" - "ciphertext-pvalues" - "federated-ciphertext-pvalues"))))) +(define hsmice-wrangled-gexp + (let ((script-profile (profile + (content (packages->manifest + (list gzip tar r r-dplyr r-genio + r-purrr r-readr r-tibble r-tidyr)))))) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (mkdir #$output) + (set-path-environment-variable + "PATH" '("bin") '(#$script-profile)) + (set-path-environment-variable + "R_LIBS_SITE" '("site-library") '(#$script-profile)) + (invoke "tar" "-xvf" #$hsmice-data + "./HSmice/1_QTL_data/") + (invoke "Rscript" + #$(local-file "../e2e-tests/hsmice/wrangle.r") + "HSmice/1_QTL_data" #$output))))) + +(define hsmice-wrangled + (computed-file "hsmice-wrangled" hsmice-wrangled-gexp)) + +(define hsmice-ciphertext-gexp + (let ((script-profile (profile + (content (packages->manifest (list pyhegp)))))) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils) + (srfi srfi-26)) + + (mkdir #$output) + (set-path-environment-variable + "PATH" '("bin") '(#$script-profile)) + (for-each (cut install-file <> (getcwd)) + (find-files #$hsmice-wrangled "\\.tsv$")) + ;; Simple data sharing workflow + (invoke "pyhegp" "encrypt" "genotype.tsv" "phenotype.tsv") + ;; Joint/federated analysis workflow + (invoke "pyhegp" "summary" "genotype1.tsv" "-o" "summary1") + (invoke "pyhegp" "summary" "genotype2.tsv" "-o" "summary2") + (invoke "pyhegp" "pool" "-o" "complete-summary" "summary1" "summary2") + (invoke "pyhegp" "encrypt" "-s" "complete-summary" "genotype1.tsv" "phenotype1.tsv") + (invoke "pyhegp" "encrypt" "-s" "complete-summary" "genotype2.tsv" "phenotype2.tsv") + (invoke "pyhegp" "cat-genotype" "-o" "complete-genotype.tsv.hegp" + "genotype1.tsv.hegp" "genotype2.tsv.hegp") + (invoke "pyhegp" "cat-phenotype" "-o" "complete-phenotype.tsv.hegp" + "phenotype1.tsv.hegp" "phenotype2.tsv.hegp") + (for-each (cut install-file <> #$output) + (find-files (getcwd) "\\.tsv.hegp$")))))) + +(define hsmice-ciphertext + (computed-file "hsmice-ciphertext" hsmice-ciphertext-gexp)) + +(define hsmice-r-mixed-model-gwas-gexp + (let ((gwas-script (local-file "../e2e-tests/hsmice/gwas.r")) + (script-profile (profile + (content (packages->manifest + (list r r-dplyr r-mixed-model-gwas + r-qqman r-readr r-stringr + r-tibble r-tidyr)))))) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (mkdir #$output) + (set-path-environment-variable + "PATH" '("bin") '(#$script-profile)) + (set-path-environment-variable + "R_LIBS_SITE" '("site-library") '(#$script-profile)) + + ;; GWAS on plaintext + (invoke "Rscript" #$gwas-script + #$(file-append hsmice-wrangled "/genotype.tsv") + #$(file-append hsmice-wrangled "/phenotype.tsv") + (string-append #$output "/plaintext-pvalues")) + (copy-file "Rplots.pdf" (string-append #$output "/plaintext-manhattan.pdf")) + + ;; GWAS with simple ciphertext data sharing + (invoke "Rscript" #$gwas-script + #$(file-append hsmice-ciphertext "/genotype.tsv.hegp") + #$(file-append hsmice-ciphertext "/phenotype.tsv.hegp") + (string-append #$output "/ciphertext-pvalues")) + (copy-file "Rplots.pdf" + (string-append #$output "/ciphertext-manhattan.pdf")) + + ;; Joint federated GWAS + (invoke "Rscript" #$gwas-script + #$(file-append hsmice-ciphertext "/complete-genotype.tsv.hegp") + #$(file-append hsmice-ciphertext "/complete-phenotype.tsv.hegp") + (string-append #$output "/federated-ciphertext-pvalues")) + (copy-file "Rplots.pdf" + (string-append #$output "/federated-ciphertext-manhattan.pdf")))))) + +(define hsmice-r-mixed-model-gwas + (computed-file "hsmice-r-mixed-model-gwas" hsmice-r-mixed-model-gwas-gexp)) + +(define hsmice-qtl-checked-gexp + (let ((script-profile (profile + (content (packages->manifest + (list python python-pandas)))))) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils) + (srfi srfi-26)) + + (mkdir #$output) + (set-path-environment-variable + "PATH" '("bin") '(#$script-profile)) + (set-path-environment-variable + "GUIX_PYTHONPATH" + '(#$(string-append "lib/python" + (version-major+minor (package-version python)) + "/site-packages")) + '(#$script-profile)) + + ;; Check that the QTL is where it should be. + (for-each (cut invoke + "python3" + #$(local-file "../e2e-tests/hsmice/check-qtl.py") + <>) + (find-files #$hsmice-r-mixed-model-gwas + "\\-pvalues$")))))) + +(define hsmice-qtl-checked + (computed-file "hsmice-qtl-checked" hsmice-qtl-checked-gexp)) (define-public hsmice-test - (computed-file "hsmice-test" hsmice-test-gexp)) + (directory-union "hsmice-test" + (list hsmice-r-mixed-model-gwas + hsmice-qtl-checked))) hsmice-test |