From 21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 17:17:48 +0100 Subject: [PATCH] gnu: ngless: Install links to required tools. * gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools. [inputs]: Add prodigal, bwa, samtools, and minimap2. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2755dba521..d9f0fe773f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14123,9 +14123,30 @@ (define-public ngless #:phases (modify-phases %standard-phases (add-after 'unpack 'create-cabal-file - (lambda _ (invoke "hpack") #t))))) + (lambda _ (invoke "hpack") #t)) + ;; 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 (string-append (assoc-ref inputs "prodigal") + "/bin/prodigal") + (string-append bin "ngless-" ,version "-prodigal")) + (symlink (string-append (assoc-ref inputs "minimap2") + "/bin/minimap2") + (string-append bin "ngless-" ,version "-minimap2")) + (symlink (string-append (assoc-ref inputs "samtools") + "/bin/samtools") + (string-append bin "ngless-" ,version "-samtools")) + (symlink (string-append (assoc-ref inputs "bwa") + "/bin/bwa") + (string-append bin "ngless-" ,version "-bwa")) + #t)))))) (inputs - `(("ghc-aeson" ,ghc-aeson) + `(("prodigal" ,prodigal) + ("bwa" ,bwa) + ("samtools" ,samtools) + ("minimap2" ,minimap2) + ("ghc-aeson" ,ghc-aeson) ("ghc-ansi-terminal" ,ghc-ansi-terminal) ("ghc-async" ,ghc-async) ("ghc-atomic-write" ,ghc-atomic-write)