Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Mon, 3 Oct 2022 00:06:02 UTC
Severity: normal
Tags: patch
Done: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Bug is archived. No further changes may be made.
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From: Liliana Marie Prikler <liliana.prikler <at> gmail.com> To: David Elsing <david.elsing <at> posteo.net>, 58261 <at> debbugs.gnu.org Subject: [bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit. Date: Sun, 09 Oct 2022 14:06:02 +0200
Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (avalontoolkit): New variable.
> ---
> gnu/packages/chemistry.scm | 93
> ++++++++++++++++++++++++++++++++++++++
> 1 file changed, 93 insertions(+)
>
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 68d28a52c3..e52dd2f3b6 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -928,3 +928,96 @@ (define-public yaehmop
> (description "@code{YAeHMOP} contains a program and library for
> performing
> extended Hückel calculations.")
> (license license:bsd-2)))
> +
> +(define-public avalontoolkit
> + (package
> + (name "avalontoolkit")
I think we could do a hyphen between avalon and toolkit.
> + (version "1.2.0")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (string-append
> + "mirror://sourceforge/avalontoolkit/"
> + "AvalonToolkit_" (substring version 0 3)
> "/AvalonToolkit_"
> + version ".source.tar"))
> + (sha256
> + (base32
> + "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
> + (modules '((guix build utils) (ice-9 ftw)))
> + (snippet
> + #~(begin
> + (chdir "..")
> + (delete-file-recursively "SourceDistribution/java")))))
> + (build-system gnu-build-system)
> + (arguments
> + (list
> + ;; There are no tests
> + #:tests? #f
> + #:phases
> + #~(let ((programs '("canonizer" "matchtest" "smi2mol"
> "struchk")))
> + (modify-phases %standard-phases
> + (delete 'configure)
> + (add-before 'build 'remove-free
> + (lambda _
> + ;; Remove incorrect free of getenv result (patch
> also in rdkit)
> + (substitute* "common/reaccsio.c"
> + (("MyFree.*tempdir.*") ""))))
> + (replace 'build
> + (lambda _
> + (chdir "common")
> + (let* ((parts
> + (list
> + "aacheck" "casutils" "denormal"
> "depictutil"
> + "didepict" "fixcharges" "forio" "geometry"
> "graph"
> + "hashcode" "layout" "local" "patclean"
> "pattern"
> + "perceive" "reaccsio" "rtutils" "set"
> "shortcut"
> + "sketch" "ssmatch" "stereo" "symbol_lists"
> + "symboltable" "utilities"))
> + (objects (map (lambda (name) (string-append
> name ".o"))
> + parts)))
> + (for-each
> + (lambda (name)
> + (display (string-append "Compiling " name
> ".c\n"))
> + (invoke "gcc" "-c" "-fPIC" "-O2"
> + (string-append name ".c")
> + "-o" (string-append name ".o")))
> + parts)
> + (display "Building shared library\n")
> + (apply invoke "gcc" "-fPIC" "-shared" "-lm"
> + "-o" "libavalontoolkit.so"
> + "canonizer.c" "smi2mol.c" "struchk.c"
> objects)
> + (for-each
> + (lambda (program)
> + (display (string-append "Building " program
> "\n"))
> + (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-
> O2"
> + (string-append "-Wl,-rpath=" #$output
> "/lib")
> + "-DMAIN" (string-append program ".c")
> "-o" program))
> + programs))))
Uhm... is the Makefile that unusable?
> + (replace 'install
> + (lambda _
> + ;; Executables
> + (for-each
> + (lambda (program)
> + (install-file program (string-append #$output
> "/bin")))
> + programs)
> + (for-each
> + (lambda (name)
> + (symlink (string-append #$output "/bin/smi2mol")
> + (string-append #$output "/bin/" name)))
> + '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma"
> "smi2rdf"))
> + ;; Library
> + (install-file "libavalontoolkit.so" (string-append
> #$output "/lib"))
> + (for-each
> + (lambda (file)
> + (install-file file (string-append #$output
> +
> "/include/avalontoolkit")))
> + (find-files "." "\\.h$"))
> + (install-file "../license.txt"
> + (string-append #$output "/share/doc/"
> + #$name "-" #$version
> "/"))))))))
Same as above.
> + (home-page "https://sourceforge.net/projects/avalontoolkit/")
> + (synopsis "Tools for SMILES and MOL files and for structure
> fingerprinting")
> + (description "This package contains a library and programs for
> +canonicalization of SMILES and MOL files, molecular structure
> fingerprinting
> +and rendering molecules.")
> + (license license:bsd-3)))
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