[PATCH] gnu: vcftools: Update to 0.1.14.

[PATCH] gnu: vcftools: Update to 0.1.14.

[Roel Janssen]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-vcftools-Update-to-0.1.14.patch --]
[-- Type: text/x-patch, Size: 3071 bytes --]

From fc68a4593db1449bb8d55a4d8edee0a0fd05ee64 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 4 Apr 2016 14:06:33 +0200
Subject: [PATCH] gnu: vcftools: Update to 0.1.14.

* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[home-page]: Update to new homepage.
---
 gnu/packages/bioinformatics.scm | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 250deb9..ff8d961 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3692,15 +3692,15 @@ Cuffdiff or Ballgown programs.")
 (define-public vcftools
   (package
     (name "vcftools")
-    (version "0.1.12b")
+    (version "0.1.14")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "mirror://sourceforge/vcftools/vcftools_"
+                    "https://github.com/vcftools/vcftools/archive/v"
                      version ".tar.gz"))
               (sha256
                (base32
-                "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
+                "1pvgv9vzlgny5h3ljcy7fl2iyn98v366kdxnxv0h36aycj20ai5s"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
@@ -3710,16 +3710,23 @@ Cuffdiff or Ballgown programs.")
                      (string-append "MANDIR=" (assoc-ref %outputs "out")
                                     "/share/man/man1"))
        #:phases
-       (alist-cons-after
-        'unpack 'patch-manpage-install
-        (lambda _
-          (substitute* "Makefile"
-            (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
-        (alist-delete 'configure %standard-phases))))
+       (modify-phases %standard-phases
+         (add-after 'configure 'patch-manpage-install
+           (lambda _
+             (substitute* "Makefile"
+               (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1"))))
+         (add-before 'configure 'run-autogen
+           (lambda _
+             (zero? (system* "sh" "autogen.sh")))))))
+    (native-inputs
+     `(("autoconf" ,(autoconf-wrapper))
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
     (inputs
      `(("perl" ,perl)
        ("zlib" ,zlib)))
-    (home-page "http://vcftools.sourceforge.net/")
+    (home-page "https://vcftools.github.io/")
     (synopsis "Tools for working with VCF files")
     (description
      "VCFtools is a program package designed for working with VCF files, such
@@ -3727,7 +3734,7 @@ as those generated by the 1000 Genomes Project.  The aim of VCFtools is to
 provide easily accessible methods for working with complex genetic variation
 data in the form of VCF files.")
     ;; The license is declared as LGPLv3 in the README and
-    ;; at http://vcftools.sourceforge.net/license.html
+    ;; at https://github.com/vcftools/vcftools/blob/master/README.md
     (license license:lgpl3)))
 
 (define-public vsearch
-- 
2.5.5


[-- Attachment #2: Type: text/plain, Size: 350 bytes --]

Dear Guix,

I would like to update 'vcftools' to 0.1.14 (the latest release).
The project now uses Autotools, so the configure phase should be run.
In addition to that, I had to run autogen.sh to generate a configure
script.

They moved from Sourceforge to Github, so I updated the source link and
the homepage to Github.

Kind regards,
Roel Janssen

Re: [PATCH] gnu: vcftools: Update to 0.1.14.

[Alex Kost]

Roel Janssen (2016-04-04 15:12 +0300) wrote:

> Dear Guix,
>
> I would like to update 'vcftools' to 0.1.14 (the latest release).
> The project now uses Autotools, so the configure phase should be run.
> In addition to that, I had to run autogen.sh to generate a configure
> script.

It happens because you use a source code "snapshot":

  https://github.com/vcftools/vcftools/archive/v0.1.14.tar.gz

Such things never contain "configure".  But look at:

  https://github.com/vcftools/vcftools/releases

There is a real release (made with "make dist"):

  https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz

It contains all the required stuff, so there is no need to use autotools
and to run "autogen.sh".

-- 
Alex

Re: [PATCH] gnu: vcftools: Update to 0.1.14.

[Roel Janssen]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-vcftools-Update-to-0.1.14.patch --]
[-- Type: text/x-patch, Size: 2849 bytes --]

From f0cc38ea5ed57018785cc20352165a7e2cd18d84 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 4 Apr 2016 20:04:48 +0200
Subject: [PATCH] gnu: vcftools: Update to 0.1.14.

* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[home-page]: Update to new homepage.
---
 gnu/packages/bioinformatics.scm | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 250deb9..0afc0a6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3692,15 +3692,15 @@ Cuffdiff or Ballgown programs.")
 (define-public vcftools
   (package
     (name "vcftools")
-    (version "0.1.12b")
+    (version "0.1.14")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "mirror://sourceforge/vcftools/vcftools_"
-                     version ".tar.gz"))
+                    "https://github.com/vcftools/vcftools/releases/download/v"
+                    version "/vcftools-" version ".tar.gz"))
               (sha256
                (base32
-                "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
+                "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
@@ -3708,18 +3708,13 @@ Cuffdiff or Ballgown programs.")
                      "CFLAGS=-O2" ; override "-m64" flag
                      (string-append "PREFIX=" (assoc-ref %outputs "out"))
                      (string-append "MANDIR=" (assoc-ref %outputs "out")
-                                    "/share/man/man1"))
-       #:phases
-       (alist-cons-after
-        'unpack 'patch-manpage-install
-        (lambda _
-          (substitute* "Makefile"
-            (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
-        (alist-delete 'configure %standard-phases))))
+                                    "/share/man/man1"))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (inputs
      `(("perl" ,perl)
        ("zlib" ,zlib)))
-    (home-page "http://vcftools.sourceforge.net/")
+    (home-page "https://vcftools.github.io/")
     (synopsis "Tools for working with VCF files")
     (description
      "VCFtools is a program package designed for working with VCF files, such
@@ -3727,7 +3722,7 @@ as those generated by the 1000 Genomes Project.  The aim of VCFtools is to
 provide easily accessible methods for working with complex genetic variation
 data in the form of VCF files.")
     ;; The license is declared as LGPLv3 in the README and
-    ;; at http://vcftools.sourceforge.net/license.html
+    ;; at https://vcftools.github.io/license.html
     (license license:lgpl3)))
 
 (define-public vsearch
-- 
2.5.5


[-- Attachment #2: Type: text/plain, Size: 1036 bytes --]

Dear Alex,

Thank you for your quick response.

Alex Kost writes:

> Roel Janssen (2016-04-04 15:12 +0300) wrote:
>
>> Dear Guix,
>>
>> I would like to update 'vcftools' to 0.1.14 (the latest release).
>> The project now uses Autotools, so the configure phase should be run.
>> In addition to that, I had to run autogen.sh to generate a configure
>> script.
>
> It happens because you use a source code "snapshot":
>
>   https://github.com/vcftools/vcftools/archive/v0.1.14.tar.gz
>
> Such things never contain "configure".  But look at:
>
>   https://github.com/vcftools/vcftools/releases
>
> There is a real release (made with "make dist"):
>
>   https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz
>
> It contains all the required stuff, so there is no need to use autotools
> and to run "autogen.sh".

I hadn't noticed the real release file.
It also seems that the manpage is installed correctly by default now, so
I removed the substitution.

The new patch is cleaner.

Kind regards,
Roel Janssen

Re: [PATCH] gnu: vcftools: Update to 0.1.14.

[Alex Kost]

Roel Janssen (2016-04-04 21:05 +0300) wrote:

> Alex Kost writes:
[...]
>> There is a real release (made with "make dist"):
>>
>>   https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz
>>
>> It contains all the required stuff, so there is no need to use autotools
>> and to run "autogen.sh".
>
> I hadn't noticed the real release file.
> It also seems that the manpage is installed correctly by default now, so
> I removed the substitution.

Right, I see.

> The new patch is cleaner.

Indeed.

> From f0cc38ea5ed57018785cc20352165a7e2cd18d84 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Mon, 4 Apr 2016 20:04:48 +0200
> Subject: [PATCH] gnu: vcftools: Update to 0.1.14.
>
> * gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
> [home-page]: Update to new homepage.
> ---
>  gnu/packages/bioinformatics.scm | 23 +++++++++--------------
>  1 file changed, 9 insertions(+), 14 deletions(-)

Applied, thanks!  I modified the commit message a bit to mention the
other changes (see commit 9b36e25¹)

¹ http://git.savannah.gnu.org/cgit/guix.git/commit/?id=9b36e256076a4c28051d0e0735e0f990c2dc0834

-- 
Alex

Re: [PATCH] gnu: vcftools: Update to 0.1.14.

[Roel Janssen]

>> From f0cc38ea5ed57018785cc20352165a7e2cd18d84 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Mon, 4 Apr 2016 20:04:48 +0200
>> Subject: [PATCH] gnu: vcftools: Update to 0.1.14.
>>
>> * gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
>> [home-page]: Update to new homepage.
>> ---
>>  gnu/packages/bioinformatics.scm | 23 +++++++++--------------
>>  1 file changed, 9 insertions(+), 14 deletions(-)
>
> Applied, thanks!  I modified the commit message a bit to mention the
> other changes (see commit 9b36e25¹)
>
> ¹ http://git.savannah.gnu.org/cgit/guix.git/commit/?id=9b36e256076a4c28051d0e0735e0f990c2dc0834

Thanks.  I will be more elaborate in future patches too.

Kind regards,
Roel Janssen