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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages mcrypt)
  #:use-module (guix packages)
  #:use-module ((guix licenses) #:select (gpl2+))
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages perl))

(define-public mcrypt
  (package
    (name "mcrypt")
    (version "2.6.8")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://sourceforge/mcrypt/MCrypt/"
                          version "/" name "-" version ".tar.gz"))
      (sha256
       (base32
        "161031n1w9pb4yzz9i47szc12a4mwpcpvyxnvafsik2l9s2aliai"))
      (patches (search-patches
                 "mcrypt-CVE-2012-4409.patch"
                 "mcrypt-CVE-2012-4426.patch"
                 "mcrypt-CVE-2012-4527.patch"))))
    (build-system gnu-build-system)
    (inputs
     `(("zlib" ,zlib)
       ("libmcrypt" ,libmcrypt)
       ("libmhash" ,libmhash)))
    (home-page "http://mcrypt.sourceforge.net/")
    (synopsis "Replacement for the popular Unix crypt command")
    (description
     "MCrypt is a replacement for the old crypt() package and crypt(1)
command, with extensions.  It allows developers to use a wide range of
encryption functions, without making drastic changes to their code.  It allows
users to encrypt files or data streams without having to be cryptographers.
The companion to MCrypt is Libmcrypt, which contains the actual encryption
functions themselves, and provides a standardized mechanism for accessing
them.")
    (license gpl2+)))

(define-public libmcrypt
  (package
    (name "libmcrypt")
    (version "2.5.8")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://sourceforge/mcrypt/Libmcrypt/" version
                          "/libmcrypt-" version ".tar.gz"))
      (sha256
       (base32
        "0gipgb939vy9m66d3k8il98rvvwczyaw2ixr8yn6icds9c3nrsz4"))))
    (build-system gnu-build-system)
    (home-page "http://mcrypt.sourceforge.net/")
    (synopsis "Encryption algorithm library")
    (description
     "Libmcrypt is a data encryption library.  The library is thread safe and
provides encryption and decryption functions.  This version of the library
supports many encryption algorithms and encryption modes.  Some algorithms
which are supported: SERPENT, RIJNDAEL, 3DES, GOST, SAFER+, CAST-256, RC2,
XTEA, 3WAY, TWOFISH, BLOWFISH, ARCFOUR, WAKE and more.")
    (license gpl2+)))

(define-public libmhash
  (package
    (name "libmhash")
    (version "0.9.9.9")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://sourceforge/mhash/mhash/" version
                          "/mhash-" version ".tar.bz2"))
      (sha256
       (base32
        "1w7yiljan8gf1ibiypi6hm3r363imm3sxl1j8hapjdq3m591qljn"))
      (patches (search-patches "mhash-keygen-test-segfault.patch"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("perl" ,perl)))                 ;for tests
    (home-page "http://mhash.sourceforge.net/")
    (synopsis "Thread-safe hash library")
    (description
     "Mhash is a thread-safe hash library, implemented in C, and provides a
uniform interface to a large number of hash algorithms.  These algorithms can
be used to compute checksums, message digests, and other signatures.  The HMAC
support implements the basics for message authentication, following RFC 2104.

Algorithms currently supplied are:

CRC-32, CRC-32B, ALDER-32, MD-2, MD-4, MD-5, RIPEMD-128, RIPEMD-160,
RIPEMD-256, RIPEMD-320, SHA-1, SHA-224, SHA-256, SHA-384, SHA-512, HAVAL-128,
HAVAL-160, HAVAL-192, HAVAL-256, TIGER, TIGER-128, TIGER-160, GOST, WHIRLPOOL,
SNEFRU-128, SNEFRU-256.")
    (license gpl2+)))
kages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Sarah Morgensen 2022-01-10gnu: python-biom-format: Remove obsolete phase....* gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Sarah Morgensen 2022-01-10gnu: python-pysam: Update to 0.18.0....* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose. Maxim Cournoyer 2022-01-10gnu: bcftools: Update to 1.14....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field. Maxim Cournoyer 2022-01-10gnu: samtools: Update to 1.14....* gnu/packages/bioinformatics.scm (samtools): Update to 1.14. [modules]: Delete argument. [phases]{install-library, install-headers}: Delete phases. This version no longer includes the legacy library (it links to htslib directly). (samtools-1.12): New variable. Maxim Cournoyer 2022-01-10gnu: htslib: Update to 1.14....* gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style. Maxim Cournoyer 2022-01-11gnu: stringtie: Update to 2.2.0....* gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0. [source]: Simplify snippet. [arguments]: Add make-flags; update build phases. [inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and libdeflate. [license]: Change to Expat license. Ricardo Wurmus 2022-01-11gnu: Add htslib-for-stringtie....* gnu/packages/bioinformatics.scm (htslib-for-stringtie): New variable. * gnu/packages/patches/htslib-for-stringtie.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Ricardo Wurmus 2022-01-04gnu: r-archr: Update to 1.0.1-1.92ab814....* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814. Ricardo Wurmus 2021-12-30gnu: Remove trailing period from synopsis....* gnu/packages/anddroid.scm (android-liblog, git-repo)[synopsis]: Remove trailing period. * gnu/packages/audio.scm (audio-to-midi)[synopsis]: Likewise. * gnu/packages/bioinformatics.scm (python-mygene, python-scanpy, nanosv)[synopsis]: Likewise. * gnu/packages/cran.scm (r-gsubfn)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-ascii-1, rust-bindgen-0.59, rust-byte-unit-4, rust-clircle-0.3, rust-dashmap-4, rust-dhcp4r-0.2, rust-fast-float-0.2, rust-fst-0.4, rust-futures-core-preview-0.3, rust-http-types-2, rust-hyper-0.14, rust-indexmap-1, rust-minimal-lexical-0.1, rust-oorandom-11.1, rust-runtime-raw-0.3, rust-sharded-slab-0.1, rust-takeable-option-0.4, rust-tower-service-0.3, rust-ttf-parser-0.12)[synopsis]: Likewise. * gnu/packages/disk.scm (f3)[synopsis]: Likewise. * gnu/packages/emacs-xyz.scm (emacs-scribble-mode, emacs-psession)[synopsis]: Likewise. * gnu/packages/golang.scm (go-github-com-kylelemons-godebug)[synopsis]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-fsnotify, ghc-libyaml, ghc-emojis, ghc-regex-tdfa, ghc-th-lift-instances, ghc-commonmark-pandoc)[synopsis]: Likewise. * gnu/packages/java.scm (java-commons-jxpath, java-jakarta-regexp)[synopsis]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-cl-annot, sbcl-envy)[synopsis]: Likewise. * gnu/packages/mail.scm (go-gitlab.com-shackra-goimapnotify)[synopsis]: Likewise. * gnu/packages/maven.scm (maven-wagon-http-shared, maven-surefire-plugin)[synopsis]: Likewise. * gnu/packages/perl.scm (perl-text-soundex)[synopsis]: Likewise. * gnu/packages/python-check.scm (python-httmock)[synopsis]: Likewise. * gnu/packages/python-web.scm (python-bottle)[synopsis]: Likewise. * gnu/packages/python-xyz.scm (python-olefile, python-tokenize-rt, python-pylzma)[synopsis]: Likewise. * gnu/packages/tex.scm (texlive-docstrip)[synopsis]: Likewise. Vagrant Cascadian 2021-12-30gnu: python-pyspoa: Fix trailing whitespace in synopsis....* gnu/packages/bioinformatics.scm (python-pyspoa)[synopsis]: Fix trailing whitespace. Vagrant Cascadian 2021-12-30gnu: lofreq: Fix trailing whitespace in synopsis....* gnu/packages/bioinformatics.scm (lofreq)[synopsis]: Fix trailing whitespace. Vagrant Cascadian 2021-12-30gnu: arriba: Fix trailing whitespace in synopsis....* gnu/packages/bioinformatics.scm (arriba)[synopsis]: Fix trailing whitespace. Vagrant Cascadian 2021-12-29gnu: ivar: Fix trailing whitespace in description....* gnu/packages/bioinformatics.scm (ivar)[description]: Fix trailing whitespace. Vagrant Cascadian