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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 84 |
1 files changed, 84 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09a64a8d4d..719f3e5f23 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3151,6 +3151,90 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.") (license license:expat))) +;; This is needed for dropseq-tools +(define-public java-picard-2.10.3 + (package + (name "java-picard") + (version "2.10.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "picard.jar" + ;; Tests require jacoco:coverage. + #:tests? #f + #:jdk ,icedtea-8 + #:main-class "picard.cmdline.PicardCommandLine" + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform) + (sxml xpath)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; This is necessary to ensure that htsjdk is found when using + ;; picard.jar as an executable. + (add-before 'build 'edit-classpath-in-manifest + (lambda* (#:key inputs #:allow-other-keys) + (chmod "build.xml" #o664) + (call-with-output-file "build.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `((target . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) + (car kids))) + ;; FIXME: We're breaking the line + ;; early with a dummy path to + ;; ensure that the store reference + ;; isn't broken apart and can still + ;; be found by the reference + ;; scanner. + (msg (format #f + "\ +Class-Path: /~a \ + ~a/share/java/htsjdk.jar${line.separator}" + ;; maximum line length is 70 + (string-tabulate (const #\b) 57) + (assoc-ref inputs "java-htsjdk")))) + (if (member "manifest" name) + `(,tag ,@kids + (echo + (@ (message ,msg) + (file "${manifest.file}") + (append "true")))) + `(,tag ,@kids))))) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build.xml.new" "build.xml") + #t))))) + (propagated-inputs + `(("java-htsjdk" ,java-htsjdk-2.10.1))) + (native-inputs + `(("java-testng" ,java-testng) + ("java-guava" ,java-guava))) + (home-page "http://broadinstitute.github.io/picard/") + (synopsis "Tools for manipulating high-throughput sequencing data and formats") + (description "Picard is a set of Java command line tools for manipulating +high-throughput sequencing (HTS) data and formats. Picard is implemented +using the HTSJDK Java library to support accessing file formats that are +commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and +VCF.") + (license license:expat))) + ;; This is the last version of Picard to provide net.sf.samtools (define-public java-picard-1.113 (package (inherit java-picard) |