02/02: gnu: ngless: Install links to required tools.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c
Author: Ricardo Wurmus <address@hidden>
Date:   Wed Nov 7 17:17:48 2018 +0100

    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 2755dba..d9f0fe7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14123,9 +14123,30 @@ absolute GSEA.")
        #: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)