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

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

[Ricardo Wurmus]

From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>

* 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)))
-- 
2.14.1

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

[Ludovic Courtès]

Ricardo Wurmus <rekado@elephly.net> skribis:

> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>
> * gnu/packages/bioinformatics.scm (paml): New variable.

LGTM, thanks!

Ludo'.

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

[Ricardo Wurmus]

> +                   (docs    '("Bismark_User_Guide.pdf"
> +                              "RELEASE_NOTES.txt")))

I removed this, because it is not used.
“guix lint” does not complain, so I pushed it to master.

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

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

[Ben Woodcroft]

Hi Ricardo,

Thanks for the package.


On 13/10/17 07:56, Ricardo Wurmus wrote:
> +         (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)
Since you've already pushed I didn't test out this package, but I notice 
that the above line is superfluous (though harmless).
ben

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

[Ricardo Wurmus]

Hi Ben,

> On 13/10/17 07:56, Ricardo Wurmus wrote:
>> +         (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)
> Since you've already pushed I didn't test out this package, but I notice 
> that the above line is superfluous (though harmless).

I removed the “docs” definition before pushing.

-- Ricardo

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

[Roel Janssen]

Ricardo Wurmus writes:

> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>
> * 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

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

[Ricardo Wurmus]

Hi Roel,

> 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.

Oh, that’s too bad.  Do you have a test case we could use to verify that
the tools work correctly after installation?

It doesn’t seem to be easy to fix this, as variables in which file names
are stored are size-restricted, and as they are copied around multiple
times it is difficult to ensure that our patch wouldn’t break things.

Here’s an untested draft of the new phases, but I suspect this would
take a lot more work:

--8<---------------cut here---------------start------------->8---
       (modify-phases %standard-phases
         (replace 'configure
           (lambda _
             (substitute* "src/BFdriver.c"
               (("/bin/bash") (which "bash")))
             (let ((share (string-append (assoc-ref outputs "out")
                                         "/share/paml/")))
               (substitute* ""
                 (("aaRatefile = dat/jones.dat"
                   (string-append "aaRatefile = "
                                  share "jones.dat"))))
               (substitute* '("src/yn00.c"
                              "src/baseml.c"
                              "src/basemlg.c"
                              "src/pamp.c"
                              "src/codeml.c"
                              "src/mcmctree.c"
                              "src/BFdriver.c")
                 (("ctlf\\[...?\\] ?= ?\"(yn00|pamp|baseml|codeml|mcmctree).ctl\"" _ file)
                  (string-append "ctlf[PATH_MAX]=\""
                                 share file ".ctl\"")))
               (substitute* "src/codeml.c"
                 (("strcpy\\(com.daafile, \"jones.dat\"\\)")
                  (string-append "strcpy(com.daafile, \""
                                 share "jones.dat\")")))
               (substitute* "src/evolver.c"
                 (("char \\*MCctlf0\\[\\]=\\{\"MCbase.dat\",\"MCcodon.dat\",\"MCaa.dat\"\\}")
                  (string-append "char *MCctlf0[]={"
                                 (string-join
                                  (map (lambda (f)
                                         (string-append "\"" share f "\""))
                                       '("MCbase.dat" "MCcodon.dat" "MCaa.dat"))
                                  ",")
                                 "}"))))
             (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"))
                   (share  (string-append (assoc-ref outputs "out")
                                          "/share/paml"))
                   (data   (append (find-files ".." "\\.(ctl|dat)$")
                                   (find-files "../dat" "\\.dat$"))))
               (mkdir-p bin)
               (for-each (lambda (file) (install-file file bin)) tools)
               (for-each (lambda (file) (install-file file share)) data)
               (copy-recursively "../doc" docdir)
               #t))))
--8<---------------cut here---------------end--------------->8---

The alternative is to just install the data files to $out/share/paml and
expect users to copy them to their current working directory.  That
seems to work.

I prefer this over patching the code, which is much too invasive.

What do you think?

-- Ricardo