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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 145 |
1 files changed, 145 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60614613bd..9c0e18591f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15316,6 +15316,151 @@ usually ignored by other methods or only used for filtering.") coordinates between different assemblies.") (license license:expat))) +(define-public ensembl-vep + (let* ((api-version "103") + (api-module + (lambda (name hash) + (origin (method git-fetch) + (uri (git-reference + (url (string-append "https://github.com/Ensembl/" + name ".git")) + (commit (string-append "release/" api-version)))) + (file-name (string-append name "-" api-version "-checkout")) + (sha256 (base32 hash)))))) + (package + (name "ensembl-vep") + (version (string-append api-version ".1")) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Ensembl/ensembl-vep.git") + (commit (string-append "release/" version)))) + (sha256 + (base32 + "1iq7p72cv9b38jz2v8a4slzy2n8y0md487943180ym9xc8qvw09c")))) + (build-system gnu-build-system) + (arguments + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (ice-9 match)) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + ;; Tests need to run after installation + (delete 'check) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((modules '(("ensembl" "/") + ("ensembl-variation" "/Variation") + ("ensembl-funcgen" "/Funcgen") + ("ensembl-io" "/"))) + (scripts '(("convert_cache.pl" "vep_convert_cache.pl") + ("INSTALL.pl" "vep_install.pl") + ("haplo" #f) + ("variant_recoder" #f) + ("filter_vep" #f) + ("vep" #f))) + (out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (perl (string-append out "/lib/perl5/site_perl"))) + (for-each + (match-lambda + ((name path) + (let ((dir (string-append perl "/Bio/EnsEMBL" path))) + (mkdir-p dir) + (copy-recursively + (string-append (assoc-ref inputs (string-append "api-module-" name)) + "/modules/Bio/EnsEMBL" path) + dir)))) + modules) + (copy-recursively "modules/" perl) + (mkdir-p bin) + (for-each + (match-lambda + ((script new-name) + (let ((location (string-append bin "/" + (or new-name (basename script))))) + (copy-file script location) + (chmod location #o555) + (wrap-program location + `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB") + ,perl)))))) + scripts) + + ;; Fix path to tools + (with-directory-excursion (string-append perl "/Bio/EnsEMBL") + (substitute* '("Funcgen/RunnableDB/ProbeMapping/PrePipelineChecks.pm" + "VEP/BaseRunner.pm" + "VEP/Utils.pm" + "VEP/AnnotationSource/Cache/VariationTabix.pm" + "VEP/AnnotationSource/Cache/BaseSerialized.pm" + "Variation/Utils/BaseVepTabixPlugin.pm" + "Variation/Utils/VEP.pm" + "Variation/Pipeline/ReleaseDataDumps/PreRunChecks.pm") + (("`which") + (string-append "`" + (assoc-ref inputs "which") + "/bin/which"))))))) + (add-after 'install 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (setenv "PERL5LIB" + (string-append (getenv "PERL5LIB") + ":" + (assoc-ref outputs "out") + "/lib/perl5/site_perl")) + (copy-recursively (string-append (assoc-ref inputs "source") "/t") + "/tmp/t") + (for-each make-file-writable (find-files "/tmp/t")) + ;; TODO: haplo needs Set/IntervalTree.pm + (invoke "perl" "-e" (string-append " +use Test::Harness; use Test::Exception; +my $dirname = \"/tmp\"; +opendir TEST, \"$dirname\\/t\"; +my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir TEST; closedir TEST; +@test_files = grep {!/Haplo/} @test_files; +runtests(@test_files); +")))))))) + (inputs + `(("bioperl-minimal" ,bioperl-minimal) + ("perl-bio-db-hts" ,perl-bio-db-hts) + ("perl-dbi" ,perl-dbi) + ("perl-dbd-mysql" ,perl-dbd-mysql) + ("perl-libwww" ,perl-libwww) + ("perl-http-tiny" ,perl-http-tiny) + ("perl-json" ,perl-json) + ("which" ,which))) + (propagated-inputs + `(("kentutils" ,kentutils))) + (native-inputs + `(("unzip" ,unzip) + ("perl" ,perl) + ("api-module-ensembl" + ,(api-module "ensembl" + "0s59rj905g72hljzfpvnx5nxwz925b917y4jp912i23f5gwxh14v")) + ("api-module-ensembl-variation" + ,(api-module "ensembl-variation" + "1dvwdzzfjhzymq02b6n4p6j3a9q4jgq0g89hs7hj1apd7zhirgkq")) + ("api-module-ensembl-funcgen" + ,(api-module "ensembl-funcgen" + "1x23pv38dmv0w0gby6rv3wds50qghb4v3v1mf43vk55msfxzry8n")) + ("api-module-ensembl-io" + ,(api-module "ensembl-io" + "14adb2x934lzsq20035mazdkhrkcw0qzb0xhz6zps9vk4wixwaix")) + ("perl-test-harness" ,perl-test-harness) + ("perl-test-exception" ,perl-test-exception))) + (home-page "http://www.ensembl.org/vep") + (synopsis "Predict functional effects of genomic variants") + (description + "This package provides a Variant Effect Predictor, which predicts +the functional effects of genomic variants. It also provides +Haplosaurus, which uses phased genotype data to predict +whole-transcript haplotype sequences, and Variant Recoder, which +translates between different variant encodings.") + (license license:asl2.0)))) + (define-public r-signac (let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c") (revision "1")) |