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authorRicardo Wurmus <rekado@elephly.net>2018-11-07 17:17:48 +0100
committerRicardo Wurmus <rekado@elephly.net>2018-11-07 17:19:53 +0100
commit21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c (patch)
tree03c6215902ab11ec55c287152b1ab59f25f48a6a
parentfff67cc8a7233179cc5e6eacb9659e7e79134111 (diff)
downloadgnu-guix-21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c.tar
gnu-guix-21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c.tar.gz
gnu: ngless: Install links to required tools.
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools. [inputs]: Add prodigal, bwa, samtools, and minimap2.
-rw-r--r--gnu/packages/bioinformatics.scm25
1 files 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 @@ 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)