* [PATCH] gnu: vcftools: Update to 0.1.14.
@ 2016-04-04 12:12 Roel Janssen
2016-04-04 17:28 ` Alex Kost
0 siblings, 1 reply; 5+ messages in thread
From: Roel Janssen @ 2016-04-04 12:12 UTC (permalink / raw)
To: guix-devel
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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
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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
^ permalink raw reply related [flat|nested] 5+ messages in thread* Re: [PATCH] gnu: vcftools: Update to 0.1.14.
2016-04-04 12:12 [PATCH] gnu: vcftools: Update to 0.1.14 Roel Janssen
@ 2016-04-04 17:28 ` Alex Kost
2016-04-04 18:05 ` Roel Janssen
0 siblings, 1 reply; 5+ messages in thread
From: Alex Kost @ 2016-04-04 17:28 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] gnu: vcftools: Update to 0.1.14.
2016-04-04 17:28 ` Alex Kost
@ 2016-04-04 18:05 ` Roel Janssen
2016-04-05 8:51 ` Alex Kost
0 siblings, 1 reply; 5+ messages in thread
From: Roel Janssen @ 2016-04-04 18:05 UTC (permalink / raw)
To: Alex Kost; +Cc: guix-devel
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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
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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
^ permalink raw reply related [flat|nested] 5+ messages in thread
end of thread, other threads:[~2016-04-05 9:15 UTC | newest]
Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
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2016-04-04 12:12 [PATCH] gnu: vcftools: Update to 0.1.14 Roel Janssen
2016-04-04 17:28 ` Alex Kost
2016-04-04 18:05 ` Roel Janssen
2016-04-05 8:51 ` Alex Kost
2016-04-05 9:15 ` Roel Janssen
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