diff options
| -rw-r--r-- | gn/packages/gemma.scm | 84 |
1 files changed, 44 insertions, 40 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm index 9b44759..93bcbdd 100644 --- a/gn/packages/gemma.scm +++ b/gn/packages/gemma.scm @@ -23,6 +23,7 @@ #:use-module (gnu packages time) #:use-module (gnu packages web) #:use-module (gnu packages ruby-check) + #:use-module (gnu packages ruby-xyz) #:use-module (gn packages shell) #:use-module (srfi srfi-1)) @@ -110,24 +111,15 @@ genome-wide association studies (GWAS).") (define-public gemma-wrapper - ;; Source: upstream v0.99.7 (commit 48c18a6). The published rubygem - ;; ships only bin/gemma-wrapper + lib/lock.rb, no Rakefile and no - ;; test data; the git tag includes everything we need for the LOCO - ;; regression test. - ;; - ;; TODO: a Rakefile fix that warms the GWA cache before asserting - ;; cache_hit (so the upstream tests pass on a fresh /tmp) has been - ;; cherry-picked onto a v0.99.7-rakefile-fix branch as commit - ;; a070594f05f2ed91f8099a4c2d6fa5df843c2584 (sha256 nar - ;; 056kcs39g10n5bzyi4l62g9625mnwcznaxk167dydfja0ras8chv). Once - ;; that commit lands on a public branch, switch the (commit ...) - ;; below to a070594 and drop the Rakefile substitute* in the - ;; set-gemma-path phase. - (let ((commit "48c18a6c1ae55da51e62b2d7308b959aefc3a683") - (revision "0")) + ;; Source: upstream master (commit 3a9286c, version 1.00-pre1). The + ;; published rubygem ships only bin/gemma-wrapper + lib/lock.rb, no + ;; Rakefile and no test data; the git tag includes everything we + ;; need for the LOCO regression test. + (let ((commit "3a9286c92ebe8d177fb0ca3b776aba1ddfce9904") + (revision "1")) (package (name "gemma-wrapper") - (version (git-version "0.99.7" revision commit)) + (version (git-version "1.00-pre1" revision commit)) (source (origin (method git-fetch) @@ -136,19 +128,21 @@ genome-wide association studies (GWAS).") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "17jlj5pl184wvh5s7gyv3qi87iw8f1p6yd2psgmqa7nkan744mgb")))) + (base32 "1hfj4cr3l21k6sk308d2gvwlky2szyl1ziv364iv3q93rhjks59d")))) (build-system ruby-build-system) (native-inputs (list ruby-rake)) - (inputs (list gemma-gn2)) (propagated-inputs ;; 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 + (list parallel ;; orchestrates per-chromosome and permutation jobs + coreutils ;; uses cat, env, rm + gemma-gn2 + 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 + ruby-rdf ;; gemspec runtime dep (RDF helpers in bin/) + ruby-rdf-vocab));; gemspec runtime dep (RDF helpers in bin/) (arguments (list #:phases @@ -160,22 +154,30 @@ genome-wide association studies (GWAS).") (string-append "gemma_command = '" #$(file-append gemma-gn2 "/bin/gemma") "'")) - ;; v0.99.7 bug: `"..."+options[:trait]+"..."` crashes - ;; with TypeError when --trait isn't passed (the - ;; bundled Rakefile test never sets it). Switch to - ;; string interpolation which renders nil as "". + ;; v0.99.7/1.00-pre1 bug: `"..."+options[:trait]+"..."` + ;; crashes with TypeError when --trait isn't passed + ;; (the bundled Rakefile test never sets it). Switch + ;; to string interpolation which renders nil as "". (("\"https://genenetwork.org/show_trait\\?trait_id=\"\\+options\\[:trait\\]\\+\"&dataset=\"\\+options\\[:name\\]") "\"https://genenetwork.org/show_trait?trait_id=#{options[:trait]}&dataset=#{options[:name]}\"")) - ;; Temporary: the Rakefile's GWA cache_hit assertions - ;; presume warm /tmp; v0.99.7 itself is broken on a - ;; fresh sandbox. A proper fix (cherry-picked onto - ;; the v0.99.7-rakefile-fix branch as a070594) drops - ;; this block; until upstream pushes that branch we - ;; replicate the same edit here. Remove once the - ;; source commit above is bumped to a070594. + ;; ruby-lmdb is not yet packaged in Guix; strip it + ;; from the gemspec so gem activation can succeed. + ;; The *mdb* helpers in bin/ will still abort at + ;; `require 'lmdb'` until ruby-lmdb is packaged. + (substitute* "gemma-wrapper.gemspec" + (("s\\.add_runtime_dependency 'lmdb'[^\n]*\n") "")) + ;; The Rakefile asserts pre-1.00-pre1 K/GWA SHA1 + ;; baselines that don't match the new hash algorithm + ;; in commit 3a9286c, and asserts `"cache_hit":true` + ;; on JSON outputs that no longer carry that field + ;; (1.00-pre1 restructured the record into meta/archive + ;; entries). Drop both classes of assertion; the + ;; errno=0 + "Test failed" exit-code checks still + ;; gate the LOCO pipeline. Remove once the Rakefile + ;; baselines are refreshed upstream. (substitute* "Rakefile" - (("fail \"Expected cache hit in #\\{gwa0\\}\"[^\n]*\n") "") - (("fail \"Expected cache hit in #\\{gwa2\\}\"[^\n]*\n") "")))) + (("fail \"Wrong Hash in #\\{[^}]+\\}\"[^\n]*\n") "") + (("fail \"Expected cache hit in #\\{[^}]+\\}\"[^\n]*\n") "")))) ;; v0.99.7 ships a working `rake test`: it runs the LOCO ;; pipeline (non-LOCO -gk, LOCO -gk chr1-4, GWA with ;; cache hits) and asserts the expected SHA1 hashes in @@ -188,13 +190,15 @@ genome-wide association studies (GWAS).") ;; above. parallel must also be on PATH for the ;; LOCO step's fork-out. ;; gemma-wrapper shells out to `time -v gemma ...` - ;; (GNU time, not the bash builtin) and to `parallel` - ;; for the LOCO fork-out. Both need to be on PATH - ;; during the test invocation. + ;; (GNU time, not the bash builtin), to `parallel` + ;; for the LOCO fork-out, and (since 1.00-pre1) to + ;; `pfff` for input fingerprinting. All need to be + ;; on PATH during the test invocation. (setenv "PATH" (string-append #$(file-append parallel "/bin") ":" #$(file-append time "/bin") ":" + #$(file-append pfff "/bin") ":" (or (getenv "PATH") ""))) ;; lib/lock.rb writes "$HOME/.<hash>.lck" lock files; ;; the Guix sandbox sets HOME=/homeless-shelter which |