Re: [PATCH] Add vcflib.

[Roel Janssen <roel@gnu.org>]

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From 80d296f9d3bc205eed06f98821bb5abd3ad8d40f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 26 Apr 2016 19:35:10 +0200
Subject: [PATCH] gnu: Add multichoose.

* gnu/packages/bioinformatics.scm (multichoose): New variable.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 620439f..b3686b6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5075,6 +5075,40 @@ the same group, and look for consistent differences between ChIP and control
 group or two ChIP groups run under different conditions.")
     (license license:gpl3+)))
 
+(define-public multichoose
+  (package
+    (name "multichoose")
+    (version "1.0.3")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/ekg/multichoose/archive/v"
+                          version ".tar.gz"))
+      (file-name (string-append name "-" version ".tar.gz"))
+      (sha256
+       (base32 "0xy86vvr3qrs4l81qis7ia1q2hnqv0xcb4a1n60smxbhqqis5w3l"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; There are no tests to run.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (install-file "multichoose" bin)
+               (install-file "multipermute" bin)))))))
+    (native-inputs
+     `(("python" ,python-2)
+       ("node" ,node)))
+    (home-page "https://github.com/ekg/multichoose")
+    (synopsis "Library for loopless multiset combination generation")
+    (description "This package provides a library implementing an efficient
+loopless multiset combination generation algorithm which is (approximately)
+described in \"Loopless algorithms for generating permutations, combinations,
+and other combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM),
+1973. (Algorithm 7.)")
+    (license license:expat)))
+
 (define-public filevercmp
   (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
     (package
-- 
2.7.4


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Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>
>> Ricardo Wurmus writes:
>>
>>> Roel Janssen <roel@gnu.org> writes:
>>>
>>>> From edcf3132dca6c3e86439710892870285377adbb2 Mon Sep 17 00:00:00 2001
>>>> From: Roel Janssen <roel@gnu.org>
>>>> Date: Tue, 22 Mar 2016 15:07:47 +0100
>>>> Subject: [PATCH 3/8] gnu: Add multichoose.
>>>
>>>> * gnu/packages/bioinformatics.scm (multichoose): New variable.
>>>> ---
>>>>  gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
>>>>  1 file changed, 35 insertions(+)
>>>
>>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>>>> index fa7ba24..9465d56 100644
>>>> --- a/gnu/packages/bioinformatics.scm
>>>> +++ b/gnu/packages/bioinformatics.scm
>>>> @@ -4861,3 +4861,38 @@ algorithm.")
>>>>        ;; this program is a submodule, is licensed MIT, which is the same as
>>>>        ;; the Expat license.
>>>>        (license (list license:gpl2 license:expat)))))
>>>> +
>>>> +(define-public multichoose
>>>> +  (package
>>>> +    (name "multichoose")
>>>> +    (version "1.0.3")
>>>> +    (source (origin
>>>> +      (method url-fetch)
>>>> +      (uri (string-append "https://github.com/ekg/multichoose/archive/v"
>>>> +                          version ".tar.gz"))
>>>> +      (file-name (string-append name "-" version ".tar.gz"))
>>>> +      (sha256
>>>> +       (base32 "0xy86vvr3qrs4l81qis7ia1q2hnqv0xcb4a1n60smxbhqqis5w3l"))))
>>>> +    (build-system gnu-build-system)
>>>> +    (native-inputs
>>>> +     `(("python" ,python-2)
>>>> +       ("node" ,node)))
>>>> +    (arguments
>>>> +     `(#:tests? #f ; There are no tests to run.
>>>> +       #:phases
>>>> +       (modify-phases %standard-phases
>>>> +         (delete 'configure) ; There is no configure phase.
>>>> +         (replace 'install
>>>> +           (lambda* (#:key outputs #:allow-other-keys)
>>>> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>>>> +               (install-file "multichoose" bin)
>>>> +               (install-file "multipermute" bin)))))))
>>>
>>> Nitpick: normally, we place the arguments right below the
>>> “build-system”.  The “native-inputs” then follow after “arguments”.
>>
>> Ok.  I fixed this in the new patch.
>>
>>>> +    (home-page "https://github.com/ekg/multichoose")
>>>> +    (synopsis "Library for efficient loopless multiset combination generation
>>>> +algorithm")
>>>
>>> This synopsis is a bit long.  Maybe drop “efficient”?  (Most projects
>>> include “efficient” or “fast” in their descriptions, so it isn’t very
>>> useful in a synopsis.)
>>
>> I dropped efficient.  A bit sad it doesn't keep the synopsis on a single
>> line.  I cannot think of a shorter way to describe this library.
>>
>>>> +    (description "A library implements an efficient loopless multiset
>>>> +combination generation algorithm which is (approximately) described in
>>>> +\"Loopless algorithms for generating permutations, combinations, and other
>>>> +combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM),
>>>> +1973. (Algorithm 7.)")
>>>
>>> “A library”?  How about “This package provides a library implementing...”
>>
>> Yes, that's better.  That reminds me to double-check descriptions for
>> complete sentences.  Thanks for catching this.
>>
>>
>> I attached a new patch.
>
> The patch looks good.  I tried to apply this to master but failed.
> Could you please try to rebase it onto master?

Yes, here it is.

Thanks!

Kind regards,
Roel Janssen