summaryrefslogtreecommitdiff
path: root/gnu
diff options
context:
space:
mode:
Diffstat (limited to 'gnu')
-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)