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 (_ _ _ _ _ _)>
>From e24f4de21ee3c367c38e431626f4796795eb9e18 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@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
