diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 71 |
1 files changed, 36 insertions, 35 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fdc87f1e80..e92611ce15 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14171,41 +14171,42 @@ datasets.") (patches (search-patches "ngless-unliftio.patch")))) (build-system haskell-build-system) (arguments - `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: - ; error: parse error on input import - ; import Options.Applicative - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'create-Versions.hs - (lambda _ - (substitute* "Makefile" - (("BWA_VERSION = .*") - (string-append "BWA_VERSION = " - ,(package-version bwa) "\n")) - (("SAM_VERSION = .*") - (string-append "SAM_VERSION = " - ,(package-version samtools) "\n")) - (("PRODIGAL_VERSION = .*") - (string-append "PRODIGAL_VERSION = " - ,(package-version prodigal) "\n")) - (("MINIMAP2_VERSION = .*") - (string-append "MINIMAP2_VERSION = " - ,(package-version minimap2) "\n"))) - (invoke "make" "NGLess/Dependencies/Versions.hs"))) - (add-after 'create-Versions.hs 'create-cabal-file - (lambda _ (invoke "hpack"))) - ;; These tools are expected to be installed alongside ngless. - (add-after 'install 'link-tools - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (symlink (search-input-file inputs "/bin/prodigal") - (string-append bin "ngless-" ,version "-prodigal")) - (symlink (search-input-file inputs "/bin/minimap2") - (string-append bin "ngless-" ,version "-minimap2")) - (symlink (search-input-file inputs "/bin/samtools") - (string-append bin "ngless-" ,version "-samtools")) - (symlink (search-input-file inputs "/bin/bwa") - (string-append bin "ngless-" ,version "-bwa")))))))) + (list + #:haddock? #f ;The haddock phase fails with: NGLess/CmdArgs.hs:20:1: + ;error: parse error on input import + ;import Options.Applicative + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'create-Versions.hs + (lambda _ + (substitute* "Makefile" + (("BWA_VERSION = .*") + (string-append "BWA_VERSION = " + #$(package-version bwa) "\n")) + (("SAM_VERSION = .*") + (string-append "SAM_VERSION = " + #$(package-version samtools) "\n")) + (("PRODIGAL_VERSION = .*") + (string-append "PRODIGAL_VERSION = " + #$(package-version prodigal) "\n")) + (("MINIMAP2_VERSION = .*") + (string-append "MINIMAP2_VERSION = " + #$(package-version minimap2) "\n"))) + (invoke "make" "NGLess/Dependencies/Versions.hs"))) + (add-after 'create-Versions.hs 'create-cabal-file + (lambda _ (invoke "hpack"))) + ;; These tools are expected to be installed alongside ngless. + (add-after 'install 'link-tools + (lambda* (#:key inputs #:allow-other-keys) + (let ((bin (string-append #$output "/bin/"))) + (symlink (search-input-file inputs "/bin/prodigal") + (string-append bin "ngless-" #$version "-prodigal")) + (symlink (search-input-file inputs "/bin/minimap2") + (string-append bin "ngless-" #$version "-minimap2")) + (symlink (search-input-file inputs "/bin/samtools") + (string-append bin "ngless-" #$version "-samtools")) + (symlink (search-input-file inputs "/bin/bwa") + (string-append bin "ngless-" #$version "-bwa")))))))) (inputs (list prodigal bwa |