[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[bug#30666] [PATCH 16/17] gnu: Add java-picard-2.10.3.
From: |
Ricardo Wurmus |
Subject: |
[bug#30666] [PATCH 16/17] gnu: Add java-picard-2.10.3. |
Date: |
Thu, 1 Mar 2018 19:41:48 +0100 |
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
---
gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 84 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 37dac291f..1dc922b67 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3167,6 +3167,90 @@ 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)
--
2.15.1
- [bug#30666] [PATCH 10/17] gnu: Add java-biojava-alignment., (continued)
- [bug#30666] [PATCH 10/17] gnu: Add java-biojava-alignment., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 08/17] gnu: Add java-forester-1.005., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 11/17] gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 03/17] gnu: Add java-jtransforms., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 09/17] gnu: Add java-biojava-phylo., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 02/17] gnu: Add java-jlargearrays., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 12/17] gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 13/17] gnu: Add java-biojava-alignment-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 14/17] gnu: Add java-htsjdk-latest., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 15/17] gnu: Add java-htsjdk-2.10.1., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 16/17] gnu: Add java-picard-2.10.3.,
Ricardo Wurmus <=
- [bug#30666] [PATCH 17/17] gnu: Add dropseq-tools., Ricardo Wurmus, 2018/03/01
- Message not available