* [bug#32138] [PATCH] gnu: Add inchi.
2018-07-13 14:10 ` Jelle Licht
@ 2018-07-13 19:01 ` Kei Kebreau
2018-07-13 21:38 ` Leo Famulari
0 siblings, 1 reply; 5+ messages in thread
From: Kei Kebreau @ 2018-07-13 19:01 UTC (permalink / raw)
To: Jelle Licht; +Cc: 32138
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Jelle Licht <jlicht@fsfe.org> writes:
> Kei Kebreau <kkebreau@posteo.net> writes:
>
>> * gnu/packages/chemistry.scm (inchi): New variable.
>> ---
>> gnu/packages/chemistry.scm | 3 +++
>> 1 file changed, 3 insertions(+)
>>
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index f1359b2cf..df79f252b 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -1,5 +1,6 @@
>> ;;; GNU Guix --- Functional package management for GNU
>> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
>> +;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
>> ;;;
>> ;;; This file is part of GNU Guix.
>> ;;;
>> @@ -20,9 +21,11 @@
>> #:use-module (guix packages)
>> #:use-module ((guix licenses) #:prefix license:)
>> #:use-module (guix download)
>> + #:use-module (gnu packages compression)
>> #:use-module (gnu packages gv)
>> #:use-module (gnu packages maths)
>> #:use-module (gnu packages python)
>> + #:use-module (guix build-system gnu)
>> #:use-module (guix build-system python))
>>
>> (define-public domainfinder
>
> It seems you forgot to commit the actual package definition :-).
Whoops! Let's try this again!
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From d132ab76417f238f914eb681a1c0f81b2375a1f9 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Fri, 13 Jul 2018 09:35:27 -0400
Subject: [PATCH] gnu: Add inchi.
* gnu/packages/chemistry.scm (inchi): New variable.
---
gnu/packages/chemistry.scm | 81 ++++++++++++++++++++++++++++++++++++++
1 file changed, 81 insertions(+)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index f1359b2cf..1a5086d62 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -20,9 +21,11 @@
#:use-module (guix packages)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
+ #:use-module (gnu packages compression)
#:use-module (gnu packages gv)
#:use-module (gnu packages maths)
#:use-module (gnu packages python)
+ #:use-module (guix build-system gnu)
#:use-module (guix build-system python))
(define-public domainfinder
@@ -54,6 +57,84 @@ single structure. The software is currently not actively maintained and works
only with Python 2 and NumPy < 1.9.")
(license license:cecill-c)))
+(define-public inchi
+ (package
+ (name "inchi")
+ (version "1.05")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.inchi-trust.org/download/"
+ (string-join (string-split version #\.) "")
+ "/INCHI-1-SRC.zip"))
+ (sha256
+ (base32
+ "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
+ (file-name (string-append name "-" version ".zip"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-before 'build 'chdir-to-build-directory
+ (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
+ (add-after 'build 'build-library
+ (lambda _
+ (chdir "../../../INCHI_API/libinchi/gcc")
+ (invoke "make")))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (doc (string-append out "/share/doc/inchi"))
+ (include-dir (string-append out "/include/inchi"))
+ (lib (string-append out "/lib/inchi"))
+ (inchi-doc (assoc-ref inputs "inchi-doc"))
+ (unzip (string-append (assoc-ref inputs "unzip")
+ "/bin/unzip")))
+ (chdir "../../..")
+ ;; Install binary.
+ (with-directory-excursion "INCHI_EXE/bin/Linux"
+ (rename-file "inchi-1" "inchi")
+ (install-file "inchi" bin))
+ ;; Install libraries.
+ (with-directory-excursion "INCHI_API/bin/Linux"
+ (for-each (lambda (file)
+ (install-file file lib))
+ (find-files "." "libinchi\\.so\\.1\\.*")))
+ ;; Install header files.
+ (with-directory-excursion "INCHI_BASE/src"
+ (for-each (lambda (file)
+ (install-file file include-dir))
+ (find-files "." "\\.h$")))
+ ;; Install documentation.
+ (mkdir-p doc)
+ (invoke unzip "-j" "-d" doc inchi-doc)
+ #t))))))
+ (native-inputs
+ `(("unzip" ,unzip)
+ ("inchi-doc"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "http://www.inchi-trust.org/download/"
+ (string-join (string-split version #\.) "")
+ "/INCHI-1-DOC.zip"))
+ (sha256
+ (base32
+ "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
+ (file-name (string-append name "-" version ".zip"))))))
+ (home-page "https://www.inchi-trust.org")
+ (synopsis "Utility for manipulating machine-readable chemical structures")
+ (description
+ "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
+chemical structures into machine-readable strings of information. InChIs are
+unique to the compound they describe and can encode absolute stereochemistry
+making chemicals and chemistry machine-readable and discoverable. A simple
+analogy is that InChI is the bar-code for chemistry and chemical structures.")
+ (license (license:non-copyleft
+ "file://LICENCE"
+ "See LICENCE in the distribution."))))
+
(define with-numpy-1.8
(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
--
2.18.0
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