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gnu: bbmap: Use gexp.

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* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
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Ricardo Wurmus 2023-01-06 15:11:48 +01:00
parent 04ea0e7de4
commit f72dc615ab
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1 changed files with 39 additions and 40 deletions
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79
gnu/packages/bioinformatics.scm
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@ -14533,50 +14533,49 @@ (define-public bbmap
"1wb94bcc006qq86x77z2rz0lc8m9f1kpnw6gdhjfg9bdaqf56rm3"))))
(build-system ant-build-system)
(arguments
`(#:build-target "dist"
#:tests? #f ; there are none
#:make-flags
,#~(list (string-append "-Dmpijar="
#$(this-package-input "java-openmpi")
"/lib/mpi.jar"))
#:modules ((guix build ant-build-system)
(list
#:build-target "dist"
#:tests? #f ; there are none
#:make-flags
#~(list (string-append "-Dmpijar="
#$(this-package-input "java-openmpi")
"/lib/mpi.jar"))
#:modules '((guix build ant-build-system)
(guix build utils)
(guix build java-utils))
#:phases
(modify-phases %standard-phases
(add-after 'build 'build-jni-library
(lambda _
(with-directory-excursion "jni"
(invoke "make" "-f" "makefile.linux"))))
;; There is no install target
(replace 'install (install-jars "dist"))
(add-after 'install 'install-scripts-and-documentation
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "calcmem.sh"
(("\\| awk ") (string-append "| " (which "awk") " ")))
(let* ((scripts (find-files "." "\\.sh$"))
(out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(doc (string-append out "/share/doc/bbmap"))
(jni (string-append out "/lib/jni")))
(substitute* scripts
(("\\$DIR\"\"docs") doc)
(("^CP=.*")
(string-append "CP=" out "/share/java/BBTools.jar\n"))
(("^NATIVELIBDIR.*")
(string-append "NATIVELIBDIR=" jni "\n"))
(("CMD=\"java")
(string-append "CMD=\"" (which "java"))))
(for-each (lambda (script) (install-file script bin)) scripts)
#:phases
#~(modify-phases %standard-phases
(add-after 'build 'build-jni-library
(lambda _
(with-directory-excursion "jni"
(invoke "make" "-f" "makefile.linux"))))
;; There is no install target
(replace 'install (install-jars "dist"))
(add-after 'install 'install-scripts-and-documentation
(lambda _
(substitute* "calcmem.sh"
(("\\| awk ") (string-append "| " (which "awk") " ")))
(let* ((scripts (find-files "." "\\.sh$"))
(bin (string-append #$output "/bin"))
(doc (string-append #$output "/share/doc/bbmap"))
(jni (string-append #$output "/lib/jni")))
(substitute* scripts
(("\\$DIR\"\"docs") doc)
(("^CP=.*")
(string-append "CP=" #$output "/share/java/BBTools.jar\n"))
(("^NATIVELIBDIR.*")
(string-append "NATIVELIBDIR=" jni "\n"))
(("CMD=\"java")
(string-append "CMD=\"" (which "java"))))
(for-each (lambda (script) (install-file script bin)) scripts)
;; Install JNI library
(install-file "jni/libbbtoolsjni.so" jni)
;; Install JNI library
(install-file "jni/libbbtoolsjni.so" jni)
;; Install documentation
(install-file "docs/readme.txt" doc)
(copy-recursively "docs/guides" doc))
#t)))
#:jdk ,openjdk11))
;; Install documentation
(install-file "docs/readme.txt" doc)
(copy-recursively "docs/guides" doc)))))
#:jdk openjdk11))
(inputs
(list gawk java-eclipse-jdt-core java-eclipse-jdt-compiler-apt
java-openmpi))