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authorJonas Meeuws <jonas.meeuws@gmail.com>2026-08-06 12:29:44 +0200
committerLiliana Marie Prikler <liliana.prikler@gmail.com>2026-08-22 16:49:16 +0200
commit43698ec2910b1477fb134a57bc58280eb4c0f424 (patch)
tree490dac8f6cc18da2484fe3a03ce90acc7b1f8cc8
parentfa593db476174190c7fec99e28b8717918ba8b0c (diff)
gnu: sambamba: Use G-Expressions.
* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Convert to list of G-Expressions. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
-rw-r--r--gnu/packages/bioinformatics.scm45
1 files changed, 23 insertions, 22 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fb95ea31a04..edf9b0acf7a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15608,28 +15608,29 @@ using high-throughput sc-RNAseq data.")
15608 "1wmka4ickrsfvkhc1mrrkxqy65g6wylsv0scmjq7m8l8qnllxbak")))) 15608 "1wmka4ickrsfvkhc1mrrkxqy65g6wylsv0scmjq7m8l8qnllxbak"))))
15609 (build-system gnu-build-system) 15609 (build-system gnu-build-system)
15610 (arguments 15610 (arguments
15611 `(#:tests? #f ; there is no test target 15611 (list
15612 #:parallel-build? #f ; not supported 15612 #:tests? #f ; there is no test target
15613 #:phases 15613 #:parallel-build? #f ; not supported
15614 (modify-phases %standard-phases 15614 #:phases
15615 (delete 'configure) 15615 #~(modify-phases %standard-phases
15616 (add-after 'unpack 'prepare-build-tools 15616 (delete 'configure)
15617 (lambda* (#:key inputs #:allow-other-keys) 15617 (add-after 'unpack 'prepare-build-tools
15618 (substitute* "Makefile" 15618 (lambda* (#:key inputs #:allow-other-keys)
15619 (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) 15619 (substitute* "Makefile"
15620 (setenv "CC" "gcc") 15620 (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
15621 (setenv "D_LD" (which "ld.gold")))) 15621 (setenv "CC" "gcc")
15622 (add-after 'unpack 'unbundle-prerequisites 15622 (setenv "D_LD" (which "ld.gold"))))
15623 (lambda _ 15623 (add-after 'unpack 'unbundle-prerequisites
15624 (substitute* "Makefile" 15624 (lambda _
15625 (("= lz4/lib/liblz4.a") "= -L-llz4") 15625 (substitute* "Makefile"
15626 (("ldc_version_info lz4-static") "ldc_version_info")))) 15626 (("= lz4/lib/liblz4.a") "= -L-llz4")
15627 (replace 'install 15627 (("ldc_version_info lz4-static") "ldc_version_info"))))
15628 (lambda* (#:key outputs #:allow-other-keys) 15628 (replace 'install
15629 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) 15629 (lambda* (#:key outputs #:allow-other-keys)
15630 (mkdir-p bin) 15630 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
15631 (copy-file (string-append "bin/sambamba-" ,base-version) 15631 (mkdir-p bin)
15632 (string-append bin "/sambamba")))))))) 15632 (copy-file (string-append "bin/sambamba-" #$base-version)
15633 (string-append bin "/sambamba"))))))))
15633 (inputs 15634 (inputs
15634 (list ldc lz4 zlib)) 15635 (list ldc lz4 zlib))
15635 (native-inputs 15636 (native-inputs