Subject: Re: [bug#28802] [PATCH] gnu: Add paml.

From: Roel Janssen <[email-masked]>
Date: Fri, 13 Oct 2017 12:22:32 +0200

Ricardo Wurmus writes:

> From: Ricardo Wurmus <[email-masked]>
>
> * gnu/packages/bioinformatics.scm (paml): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 50 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 9a47b076c..2de57d447 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -10085,3 +10085,53 @@ straight away.  Its main features are:
>    and CHH context
>  @end itemize\n")
>      (license license:gpl3+)))
> +
> +(define-public paml
> +  (package
> +    (name "paml")
> +    (version "4.9e")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
> +                                  "paml" version ".tgz"))
> +              (sha256
> +               (base32
> +                "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
> +              (modules '((guix build utils)))
> +              ;; Remove Windows binaries
> +              (snippet
> +               '(begin
> +                  (for-each delete-file (find-files "." "\\.exe$"))
> +                  #t))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     `(#:tests? #f ; there are no tests
> +       #:make-flags '("CC=gcc")
> +       #:phases
> +       (modify-phases %standard-phases
> +         (replace 'configure
> +           (lambda _
> +             (substitute* "src/BFdriver.c"
> +               (("/bin/bash") (which "bash")))
> +             (chdir "src")
> +             #t))
> +         (replace 'install
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let ((tools '("baseml" "basemlg" "codeml"
> +                            "pamp" "evolver" "yn00" "chi2"))
> +                   (bin    (string-append (assoc-ref outputs "out") "/bin"))
> +                   (docdir (string-append (assoc-ref outputs "out")
> +                                           "/share/doc/paml"))
> +                   (docs    '("Bismark_User_Guide.pdf"
> +                              "RELEASE_NOTES.txt")))
> +               (mkdir-p bin)
> +               (for-each (lambda (file) (install-file file bin)) tools)
> +               (copy-recursively "../doc" docdir)
> +               #t))))))
> +    (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
> +    (synopsis "Phylogentic analysis by maximum likelihood")
> +    (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
> +contains a few programs for model fitting and phylogenetic tree reconstruction
> +using nucleotide or amino-acid sequence data.")
> +    ;; GPLv3 only
> +    (license license:gpl3)))

I guess I'm too late already.  I had a similar patch, but the program
uses the data files it ships with, and expects them to be in the same
location.  So this patch seems incomplete to me.

Anyway.. it has already been pushed.

Kind regards,
Roel Janssen