* [PATCH] Add diamond
@ 2015-06-17 1:56 Ben Woodcroft
2015-06-17 4:13 ` Mark H Weaver
2015-06-17 4:54 ` Mark H Weaver
0 siblings, 2 replies; 5+ messages in thread
From: Ben Woodcroft @ 2015-06-17 1:56 UTC (permalink / raw)
To: guix-devel@gnu.org
[-- Attachment #1: Type: text/plain, Size: 3820 bytes --]
Hi,
I'm quite new, so I strongly suspect there might be fixups required, but
it works on my box. Well, it works on my setup in an isolated .scm file,
but I wasn't sure how to test after I had patched bioinformatics.scm
i.e. I expected the following to work. Thanks, there's a couple more
patches (and questions..) to submit once I've learned from this one.
ben@u:~/git/guix$ GUIX_PACKAGE_PATH=/home/ben/git/guix guix package -i
diamond --verbose -K
warning: failed to install locale: Invalid argument
;;; note: source file /home/ben/git/guix/gnu/packages/base.scm
;;; newer than compiled
/home/ben/.config/guix/latest/gnu/packages/base.go
;;; note: source file /home/ben/git/guix/gnu/packages/acl.scm
;;; newer than compiled
/home/ben/.config/guix/latest/gnu/packages/acl.go
...
guix package: warning: failed to load '(build-aux build-self)':
ERROR: no code for module (build-aux build-self)
guix package: warning: failed to load '(build-aux
check-available-binaries)': exception thrown: #<condition &message
[message: "python-disable-ssl-test.patch: patch not found"] 23501e0>
checking final inputs for 'x86_64-linux'...
substitute: warning: failed to install locale: Invalid argument
checking final inputs for 'i686-linux'...
checking final inputs for 'mips64el-linux'...
guix package: warning: failed to load '(build-aux
check-final-inputs-self-contained)':
ERROR: no code for module (build-aux check-final-inputs-self-contained)
guix package: warning: failed to load '(build-aux download)':
guix package: warning: failed to load '(build-aux build-self)':
ERROR: Wrong number of arguments to #<procedure display-error (_ _ _ _ _ _)>
guix package: warning: failed to load '(build-aux
check-available-binaries)': exception thrown: #<condition &message
[message: "python-disable-ssl-test.patch: patch not found"] 689fda0>
guix package: warning: failed to load '(build-aux
check-final-inputs-self-contained)':
ERROR: no code for module (build-aux check-final-inputs-self-contained)
guix package: warning: failed to load '(build-aux download)':
Backtrace:
In ice-9/boot-9.scm:
1724: 19 [%start-stack load-stack ...]
1729: 18 [#<procedure 13aeea0 ()>]
In unknown file:
?: 17 [primitive-load "/usr/local/bin/guix"]
In guix/ui.scm:
1015: 16 [run-guix-command package "-i" "diamond" "--verbose" "-K"]
In ice-9/boot-9.scm:
157: 15 [catch srfi-34 #<procedure 404b3a0 at guix/ui.scm:377:2 ()> ...]
157: 14 [catch system-error ...]
In guix/scripts/package.scm:
1045: 13 [#<procedure 4378f30 at guix/scripts/package.scm:1034:4 ()>]
904: 12 [process-actions (# # # # ...)]
656: 11 [options->installable (# # # # ...) #<<manifest> entries: #>]
In srfi/srfi-1.scm:
664: 10 [filter-map #<procedure 40432a0 at
guix/scripts/package.scm:656:16 (expr)> ...]
In guix/scripts/package.scm:
662: 9 [#<procedure 40432a0 at guix/scripts/package.scm:656:16 (expr)> #]
347: 8 [specification->package+output "diamond" "out"]
In gnu/packages.scm:
259: 7 [find-best-packages-by-name "diamond" #f]
In guix/utils.scm:
428: 6 [#<procedure 1d80ba0 at guix/utils.scm:424:4 args>]
In gnu/packages.scm:
208: 5 [fold-packages #<procedure 1ac62a0 at gnu/packages.scm:241:20
(p r)> #]
In srfi/srfi-1.scm:
481: 4 [fold-right #<procedure 1ac6740 at gnu/packages.scm:179:14
(spec result)> ...]
In gnu/packages.scm:
182: 3 [#<procedure 1ac6740 at gnu/packages.scm:179:14 (spec result)>
"/home/ben/git/guix" ...]
In srfi/srfi-1.scm:
664: 2 [filter-map #<procedure 28823a0 at gnu/packages.scm:162:14
(file)> #]
In gnu/packages.scm:
170: 1 [#<procedure 68bea80 at gnu/packages.scm:168:20 args>
match-error ...]
In unknown file:
?: 0 [display-error #f #<output: file /dev/pts/20> ...]
ERROR: In procedure display-error:
ERROR: Wrong number of arguments to #<procedure display-error (_ _ _ _ _ _)>
[-- Attachment #2: 0001-gnu-Add-diamond.patch --]
[-- Type: text/x-patch, Size: 2732 bytes --]
From e24f4de21ee3c367c38e431626f4796795eb9e18 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 17 Jun 2015 11:49:27 +1000
Subject: [PATCH] gnu: Add diamond.
* gnu/packages/bioinformatics.scm (diamond): New variable.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d8a6d5..94db812 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,7 @@
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
+ #:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
@@ -615,6 +616,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
+(define-public diamond
+ (package
+ (name "diamond")
+ (version "0.7.9")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://github.com/bbuchfink/diamond/archive/v" version ".tar.gz"))
+ (sha256
+ (base32
+ "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:phases
+ (alist-cons-after
+ 'unpack 'enter-source-dir
+ (lambda _ (chdir "src"))
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append
+ (assoc-ref outputs "out") "/bin")))
+ (mkdir-p bin)
+ (copy-file "../bin/diamond" (string-append bin "/diamond"))))
+ (alist-delete 'configure %standard-phases)))))
+ (native-inputs
+ `(("bc" ,bc)))
+ (inputs
+ `(("boost" ,boost)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/bbuchfink/diamond")
+ (synopsis "Accelerated BLAST compatible local sequence aligner")
+ (description
+ "DIAMOND is a BLAST-compatible local aligner for mapping protein and
+translated DNA query sequences against a protein reference database (BLASTP
+and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
+reads at a typical sensitivity of 90-99% relative to BLAST depending on the
+data and settings.")
+ (license (license:non-copyleft (string-append "https://github.com/bbuchfink"
+ "/diamond/blob/v"
+ version
+ "/src/COPYING")))))
+
(define-public edirect
(package
(name "edirect")
--
2.1.4
^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCH] Add diamond
2015-06-17 1:56 [PATCH] Add diamond Ben Woodcroft
@ 2015-06-17 4:13 ` Mark H Weaver
2015-06-17 4:54 ` Mark H Weaver
1 sibling, 0 replies; 5+ messages in thread
From: Mark H Weaver @ 2015-06-17 4:13 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> I'm quite new, so I strongly suspect there might be fixups required,
> but it works on my box. Well, it works on my setup in an isolated .scm
> file, but I wasn't sure how to test after I had patched
> bioinformatics.scm i.e. I expected the following to work. Thanks,
> there's a couple more patches (and questions..) to submit once I've
> learned from this one.
>
> ben@u:~/git/guix$ GUIX_PACKAGE_PATH=/home/ben/git/guix guix package -i
> diamond --verbose -K
If you modified the files in the git repo directly, then just do this:
./pre-inst-env guix build -K diamond
and if that succeeds:
./pre-inst-env guix package -i diamond
GUIX_PACKAGE_PATH is only needed if you're _not_ working from a git
repo, and in that case you want to point it to a directory that contains
_only_ *.scm files with your out-of-tree package descriptions, nothing
else.
The problem you ran into is that Guix will attempt to load every *.scm
file in that directory tree looking for package descriptions, and it
does not cope well with other things being in there like build-aux/*.scm
Mark
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Add diamond
2015-06-17 1:56 [PATCH] Add diamond Ben Woodcroft
2015-06-17 4:13 ` Mark H Weaver
@ 2015-06-17 4:54 ` Mark H Weaver
2015-06-17 9:25 ` Ben Woodcroft
1 sibling, 1 reply; 5+ messages in thread
From: Mark H Weaver @ 2015-06-17 4:54 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> From e24f4de21ee3c367c38e431626f4796795eb9e18 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Wed, 17 Jun 2015 11:49:27 +1000
> Subject: [PATCH] gnu: Add diamond.
>
> * gnu/packages/bioinformatics.scm (diamond): New variable.
> ---
> gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 46 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 0d8a6d5..94db812 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
Please add a copyright line for yourself to the top of the file.
> @@ -28,6 +28,7 @@
> #:use-module (guix build-system python)
> #:use-module (guix build-system trivial)
> #:use-module (gnu packages)
> + #:use-module (gnu packages algebra)
> #:use-module (gnu packages base)
> #:use-module (gnu packages boost)
> #:use-module (gnu packages compression)
> @@ -615,6 +616,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
> other types of unwanted sequence from high-throughput sequencing reads.")
> (license license:expat)))
>
> +(define-public diamond
> + (package
> + (name "diamond")
> + (version "0.7.9")
> + (source (origin
> + (method url-fetch)
> + (uri
> + (string-append
> + "https://github.com/bbuchfink/diamond/archive/v" version ".tar.gz"))
Please add:
(file-name (string-append name "-" version ".tar.gz"))
to this 'origin' form, because otherwise the filename of the source
tarball in the store will be /gnu/store/…-v0.7.9.tar.gz without the name
of the package. By default it is named based on the last path component
of the source URI.
> + (sha256
> + (base32
> + "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))))
It would be good to remove the pre-compiled binary by adding the
following snippet to the 'origin' form:
--8<---------------cut here---------------start------------->8---
(snippet '(begin
(delete-file "bin/diamond")
#t))
--8<---------------cut here---------------end--------------->8---
> + (build-system gnu-build-system)
> + (arguments
> + '(#:tests? #f ;no "check" target
> + #:phases
Please use spaces instead of tabs, and align "#:phases" directly under
"#:tests?".
> + (alist-cons-after
> + 'unpack 'enter-source-dir
> + (lambda _ (chdir "src"))
Phase procedures should return a boolean indicating whether the phase
succeeded, but the return value of 'chdir' is unspecified. So you
should add #t after (chdir "src").
> + (alist-replace
> + 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let ((bin (string-append
> + (assoc-ref outputs "out") "/bin")))
> + (mkdir-p bin)
> + (copy-file "../bin/diamond" (string-append bin "/diamond"))))
Our convention is to have the body of a lambda indented two columns more
than the lambda itself, so the open paren of the 'let' should be under
the 'a' in 'lambda'. Add #t to the end. Please try to keep lines <= 80
columns.
> + (alist-delete 'configure %standard-phases)))))
It would also be good to use our new and improved 'modify-phases'
syntax. Search for it in gnu/packages/*.scm for examples.
> + (native-inputs
> + `(("bc" ,bc)))
> + (inputs
> + `(("boost" ,boost)
> + ("zlib" ,zlib)))
> + (home-page "https://github.com/bbuchfink/diamond")
> + (synopsis "Accelerated BLAST compatible local sequence aligner")
> + (description
> + "DIAMOND is a BLAST-compatible local aligner for mapping protein and
> +translated DNA query sequences against a protein reference database (BLASTP
> +and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
Please put two spaces between sentences.
> +reads at a typical sensitivity of 90-99% relative to BLAST depending on the
> +data and settings.")
> + (license (license:non-copyleft (string-append "https://github.com/bbuchfink"
> + "/diamond/blob/v"
> + version
> + "/src/COPYING")))))
(license (license:non-copyleft "file://src/COPYING"
"See src/COPYING in the distribution."))))
I wouldn't normally do this, but I went ahead and tested it with these
changes and here's what it comes out to:
--8<---------------cut here---------------start------------->8---
(define-public diamond
(package
(name "diamond")
(version "0.7.9")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/bbuchfink/diamond/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
(snippet '(begin
(delete-file "bin/diamond")
#t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-source-dir
(lambda _
(chdir "src")
#t))
(delete 'configure)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p bin)
(copy-file "../bin/diamond"
(string-append bin "/diamond"))
#t))))))
(native-inputs
`(("bc" ,bc)))
(inputs
`(("boost" ,boost)
("zlib" ,zlib)))
(home-page "https://github.com/bbuchfink/diamond")
(synopsis "Accelerated BLAST compatible local sequence aligner")
(description
"DIAMOND is a BLAST-compatible local aligner for mapping protein and
translated DNA query sequences against a protein reference database (BLASTP
and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
data and settings.")
(license (license:non-copyleft "file://src/COPYING"
"See src/COPYING in the distribution."))))
--8<---------------cut here---------------end--------------->8---
but feel free to do it a bit differently :) Anyway, can you send an
updated patch? Don't forget your copyright notice.
Thanks!
Mark
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Add diamond
2015-06-17 4:54 ` Mark H Weaver
@ 2015-06-17 9:25 ` Ben Woodcroft
2015-06-17 23:48 ` Mark H Weaver
0 siblings, 1 reply; 5+ messages in thread
From: Ben Woodcroft @ 2015-06-17 9:25 UTC (permalink / raw)
To: Mark H Weaver; +Cc: guix-devel@gnu.org
[-- Attachment #1: Type: text/plain, Size: 312 bytes --]
On 17/06/15 14:54, Mark H Weaver wrote:
> I wouldn't normally do this, but I went ahead and tested it with these
> changes and here's what it comes out to:
Thanks very much for taking the time to do this. I've attached the
updated patch. Wasn't sure if there a standard way to thank you in the
commit message?
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-diamond.patch --]
[-- Type: text/x-patch; name="0001-gnu-Add-diamond.patch", Size: 3483 bytes --]
From 7542d5eac8b8c813569f57a223f34de45f47edf6 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 17 Jun 2015 19:21:22 +1000
Subject: [PATCH] gnu: Add diamond.
* gnu/packages/bioinformatics.scm (diamond): New variable.
---
gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 52 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d8a6d5..5c75374 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -28,6 +29,7 @@
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
+ #:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
@@ -615,6 +617,56 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
+(define-public diamond
+ (package
+ (name "diamond")
+ (version "0.7.9")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/bbuchfink/diamond/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
+ (snippet '(begin
+ (delete-file "bin/diamond")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-source-dir
+ (lambda _
+ (chdir "src")
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-file "../bin/diamond"
+ (string-append bin "/diamond"))
+ #t))))))
+ (native-inputs
+ `(("bc" ,bc)))
+ (inputs
+ `(("boost" ,boost)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/bbuchfink/diamond")
+ (synopsis "Accelerated BLAST compatible local sequence aligner")
+ (description
+ "DIAMOND is a BLAST-compatible local aligner for mapping protein and
+translated DNA query sequences against a protein reference database (BLASTP
+and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
+reads at a typical sensitivity of 90-99% relative to BLAST depending on the
+data and settings.")
+ (license (license:non-copyleft "file://src/COPYING"
+ "See src/COPYING in the distribution."))))
+
(define-public edirect
(package
(name "edirect")
--
2.1.4
^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCH] Add diamond
2015-06-17 9:25 ` Ben Woodcroft
@ 2015-06-17 23:48 ` Mark H Weaver
0 siblings, 0 replies; 5+ messages in thread
From: Mark H Weaver @ 2015-06-17 23:48 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> On 17/06/15 14:54, Mark H Weaver wrote:
>> I wouldn't normally do this, but I went ahead and tested it with these
>> changes and here's what it comes out to:
> Thanks very much for taking the time to do this. I've attached the
> updated patch.
Pushed, thanks!
> Wasn't sure if there a standard way to thank you in the
> commit message?
No need, but thanks for asking.
Mark
^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2015-06-17 23:49 UTC | newest]
Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
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2015-06-17 1:56 [PATCH] Add diamond Ben Woodcroft
2015-06-17 4:13 ` Mark H Weaver
2015-06-17 4:54 ` Mark H Weaver
2015-06-17 9:25 ` Ben Woodcroft
2015-06-17 23:48 ` Mark H Weaver
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