diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 83 |
1 files changed, 41 insertions, 42 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b43e166441..b05ddd44e2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14533,50 +14533,49 @@ is a Cython wrapper for FIt-SNE.") "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) - - ;; 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)) + #: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 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)) |