diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2018-11-07 17:17:48 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-11-07 17:19:53 +0100 |
| commit | 21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c (patch) | |
| tree | 03c6215902ab11ec55c287152b1ab59f25f48a6a | |
| parent | fff67cc8a7233179cc5e6eacb9659e7e79134111 (diff) | |
| download | patches-21335fdbec68b4cfb19d8a0ae0877ec81c84ad9c.tar patches-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.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) |