diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
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) |