* [bug#28802] [PATCH] gnu: Add paml.
@ 2017-10-12 21:56 Ricardo Wurmus
2017-10-13 8:51 ` Ludovic Courtès
` (3 more replies)
0 siblings, 4 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2017-10-12 21:56 UTC (permalink / raw)
To: 28802; +Cc: 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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#28802] [PATCH] gnu: Add paml.
2017-10-12 21:56 [bug#28802] [PATCH] gnu: Add paml Ricardo Wurmus
@ 2017-10-13 8:51 ` Ludovic Courtès
2017-10-13 9:15 ` bug#28802: " Ricardo Wurmus
` (2 subsequent siblings)
3 siblings, 0 replies; 7+ messages in thread
From: Ludovic Courtès @ 2017-10-13 8:51 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Ricardo Wurmus, 28802
Ricardo Wurmus <rekado@elephly.net> skribis:
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>
> * gnu/packages/bioinformatics.scm (paml): New variable.
LGTM, thanks!
Ludo'.
^ permalink raw reply [flat|nested] 7+ messages in thread
* bug#28802: [PATCH] gnu: Add paml.
2017-10-12 21:56 [bug#28802] [PATCH] gnu: Add paml Ricardo Wurmus
2017-10-13 8:51 ` Ludovic Courtès
@ 2017-10-13 9:15 ` Ricardo Wurmus
2017-10-13 9:23 ` [bug#28802] " Ben Woodcroft
2017-10-13 10:22 ` Roel Janssen
3 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2017-10-13 9:15 UTC (permalink / raw)
To: 28802-done
> + (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
^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#28802] [PATCH] gnu: Add paml.
2017-10-12 21:56 [bug#28802] [PATCH] gnu: Add paml Ricardo Wurmus
2017-10-13 8:51 ` Ludovic Courtès
2017-10-13 9:15 ` bug#28802: " Ricardo Wurmus
@ 2017-10-13 9:23 ` Ben Woodcroft
2017-10-13 9:35 ` Ricardo Wurmus
2017-10-13 10:22 ` Roel Janssen
3 siblings, 1 reply; 7+ messages in thread
From: Ben Woodcroft @ 2017-10-13 9:23 UTC (permalink / raw)
To: Ricardo Wurmus, 28802; +Cc: Ricardo Wurmus
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#28802] [PATCH] gnu: Add paml.
2017-10-13 9:23 ` [bug#28802] " Ben Woodcroft
@ 2017-10-13 9:35 ` Ricardo Wurmus
0 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2017-10-13 9:35 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: 28802
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#28802] [PATCH] gnu: Add paml.
2017-10-12 21:56 [bug#28802] [PATCH] gnu: Add paml Ricardo Wurmus
` (2 preceding siblings ...)
2017-10-13 9:23 ` [bug#28802] " Ben Woodcroft
@ 2017-10-13 10:22 ` Roel Janssen
2017-10-13 13:25 ` Ricardo Wurmus
3 siblings, 1 reply; 7+ messages in thread
From: Roel Janssen @ 2017-10-13 10:22 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Ricardo Wurmus, 28802
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#28802] [PATCH] gnu: Add paml.
2017-10-13 10:22 ` Roel Janssen
@ 2017-10-13 13:25 ` Ricardo Wurmus
0 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2017-10-13 13:25 UTC (permalink / raw)
To: Roel Janssen; +Cc: Ricardo Wurmus, 28802
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
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2017-10-13 13:26 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz / follow: Atom feed)
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2017-10-12 21:56 [bug#28802] [PATCH] gnu: Add paml Ricardo Wurmus
2017-10-13 8:51 ` Ludovic Courtès
2017-10-13 9:15 ` bug#28802: " Ricardo Wurmus
2017-10-13 9:23 ` [bug#28802] " Ben Woodcroft
2017-10-13 9:35 ` Ricardo Wurmus
2017-10-13 10:22 ` Roel Janssen
2017-10-13 13:25 ` Ricardo Wurmus
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