Moving to guix-bioinformatics-past

7 files changed, 0 insertions, 450 deletions

diff --git a/gn/packages/binderlite.scm b/gn/packages/binderlite.scm
deleted file mode 100644
index 8010e41..0000000
--- a/gn/packages/binderlite.scm
+++ /dev/null
@@ -1,37 +0,0 @@
-(define-module (gn packages binderlite)
-  #:use-module (gnu packages)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (gnu packages python-web)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix utils)
-  #:use-module (guix build-system asdf)
-  #:use-module (guix build-system python))
-
-(define-public python-jgart-giturlparse
-  ;; https://github.com/nephila/giturlparse/pull/41
-  (let ((commit "719f4c8e642718121f5a7b91ae8160b0041d31f9")
-        (revision "0"))
-    (package
-      (inherit python-giturlparse)
-      (name "python-jgart-giturlparse")
-      (version (git-version "20211107" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://git.genenetwork.org/jgart/giturlparse")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "1nyp0gw48cmnkcccgvq14adsykf9sk0z34x3j2myfm9g9cg9d669"))))
-          (arguments (list #:tests? #f))
-          (description
-"Provides an updated clean_data function for the github platform.  See
-@url{https://github.com/nephila/giturlparse/pull/41}.  @code{binderlite}
-will be rewritten in Common Lisp.  If we stay with Python I recommend
-switching this library out for @code{python-furl} or similar."))))
-
diff --git a/gn/packages/gitea.scm b/gn/packages/gitea.scm
deleted file mode 100644
index 6a6e8a9..0000000
--- a/gn/packages/gitea.scm
+++ /dev/null
@@ -1,79 +0,0 @@
-(define-module (gn packages gitea)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix build-system go)
-  #:use-module (gnu packages bash)
-  #:use-module (gnu packages node)
-  #:use-module (gnu packages version-control))
-
-(define-public gitea
-  (package
-    (name "gitea")
-    (version "1.15.11")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/go-gitea/gitea/releases"
-                                  "/download/v" version
-                                  "/gitea-src-" version ".tar.gz"))
-              (sha256
-               (base32 "0ihw68qy36xdwp6kiardxlbp1x0s10gjdkg51b6p93c0r9pm9501"))))
-    (build-system go-build-system)
-    (arguments
-     `(#:install-source? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'patch-source-shebangs 'unpatch-example-shebangs
-           ;; If we don't do this then git repos created with this version of
-           ;; gitea will use the build environment's bash for the different
-           ;; git repo hooks.
-           (lambda _
-             (substitute*
-               (find-files "src/integrations/gitea-repositories-meta"
-                           "(\\.sample|gitea|(post|pre)-receive|update)")
-               (("#!/gnu/store/.*/bin/bash") "#!/bin/bash")
-               (("#!/gnu/store/.*/bin/sh") "#!/bin/sh"))))
-         (add-before 'build 'prepare-build
-           (lambda _
-             (setenv "TAGS" "bindata sqlite sqlite_unlock_notify")))
-         (replace 'build
-           (lambda _
-             (with-directory-excursion "src"
-               (invoke "make" "build")
-               (invoke "make" "generate-manpage"))))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (with-directory-excursion "src"
-                 (invoke "make" "test-backend")
-                 ;; Gitea requires git with lfs support to run tests.
-                 ;(invoke "make" "test-sqlite")
-                 (invoke "make" "test-sqlite-migration")))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (with-directory-excursion "src"
-                 (invoke "make" "install")
-                 (install-file "man/man1/gitea.1.gz"
-                               (string-append out "/share/man/man1"))))))
-         (add-after 'install 'wrap-program
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin/gitea")))
-               (wrap-program bin
-                 `("PATH" ":" prefix
-                   (,(dirname (search-input-file inputs "/bin/git")))))))))))
-    ;(native-inputs
-    ; (list node-lts))
-    (inputs
-     (list bash-minimal
-           git))
-    (home-page "https://gitea.io/")
-    (synopsis "Self-hosted git service")
-    (description "Gitea is an open-source forge software package for hosting
-software development version control using Git as well as other collaborative
-features like bug tracking, wikis and code review.")
-    (properties
-      '((release-monitoring-url . "https://github.com/go-gitea/gitea/releases")))
-    (license license:expat)))
diff --git a/gn/packages/globus.scm b/gn/packages/globus.scm
deleted file mode 100644
index a8c9212..0000000
--- a/gn/packages/globus.scm
+++ /dev/null
@@ -1,76 +0,0 @@
-(define-module (gn packages globus)
-  #:use-module (gnu packages check)
-  #:use-module (gnu packages python-build)
-  #:use-module (gnu packages python-crypto)
-  #:use-module (gnu packages python-web)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
-  #:use-module (guix download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages))
-
-(define-public python-click-type-test
-  (package
-    (name "python-click-type-test")
-    (version "0.0.7")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "click-type-test" version))
-              (sha256
-               (base32
-                "1i3z7akiz7s8jy6x0vzrak88m55ac1spq88vziwryzr7355y3hgq"))))
-    (build-system pyproject-build-system)
-    (native-inputs (list python-pytest))
-    (propagated-inputs (list python-click))
-    (home-page "https://github.com/sirosen/click-type-test")
-    (synopsis "Test that type annotations match click parameter types")
-    (description "@code{python-click-type-test} allows you to test that your click
-options and arguments match your type annotations.")
-    (license license:expat)))
-
-(define-public globus-cli
-  (package
-    (name "globus-cli")
-    (version "3.25.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "globus-cli" version))
-              (sha256
-               (base32
-                "05div2psajmqdy9md804q4x6ha4yfp4w6yrxz0ynsq3i62a6cl5v"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list #:tests? #f))
-    (propagated-inputs
-     (list python-click
-           python-cryptography
-           python-globus-sdk
-           python-jmespath
-           python-packaging
-           python-requests
-           python-typing-extensions))
-    (home-page "https://docs.globus.org/cli")
-    (synopsis "Globus CLI")
-    (description "@code{globus-cli} provides a command-line interface to
-Globus APIs.")
-    (license license:asl2.0)))
-
-(define-public python-globus-sdk
-  (package
-    (name "python-globus-sdk")
-    (version "3.37.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "globus-sdk" version))
-              (sha256
-               (base32
-                "19w3pjzfycaqvvr11nq8c91i6pkkkic95yf170hr39dwj70lrkc7"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-cryptography python-pyjwt python-requests
-                             python-typing-extensions))
-    (home-page "https://github.com/globus/globus-sdk-python")
-    (synopsis "Globus SDK for Python")
-    (description "@code{python-globus-sdk} provides a convenient Pythonic interface to
-Globus APIs.")
-    (license license:asl2.0)))
diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm
deleted file mode 100644
index d0e9127..0000000
--- a/gn/packages/hyphy.scm
+++ /dev/null
@@ -1,71 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
-;;; Copyright © 2019 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 (gn packages hyphy)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix packages)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages curl)
-  #:use-module (gnu packages mpi)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages tls))
-
-;; TODO: Unbundle sqlite, gtest
-(define-public hyphy ; guix: check
-  (package
-    (name "hyphy")
-    (version "2.5.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/veg/hyphy.git")
-                     (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1fvmwg2rxkz3abhhldiir69vmyc4i85vdvy64bizgxd0g2k2bikm"))))
-    (inputs
-     `(("curl" ,curl)
-       ("fftw-openmpi" ,fftw-openmpi)
-       ("openmpi" ,openmpi)
-       ("openssl" ,openssl)
-       ("python" ,python-2)))
-    (build-system cmake-build-system)
-    (arguments
-     '(#:make-flags '("MPI") ; Add "GTEST" for tests, currently fails to compile.
-       #:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
-                               (string-append "-DINSTALL_PREFIX="
-                                              (assoc-ref %outputs "out")))
-       #:tests? #f
-       #:test-target "HYPHYGTEST"))
-    (synopsis "hyphy: an open-source software package for the analysis
-of genetic sequences using techniques in phylogenetics, molecular
-evolution, and machine learning.")
-    (description "HyPhy is an open-source software package for the
-analysis of genetic sequences using techniques in phylogenetics,
-molecular evolution, and machine learning.  It features a complete
-graphical user interface (GUI) and a rich scripting language for
-limitless customization of analyses. Additionally, HyPhy features
-support for parallel computing environments (via message passing
-interface (MPI)) and it can be compiled as a shared library and called
-from other programming environments such as Python and R. ")
-    (home-page "http://hyphy.org")
-    (license license:expat)))
diff --git a/gn/packages/opencl-icd-loader.scm b/gn/packages/opencl-icd-loader.scm
deleted file mode 100644
index 5e17d2f..0000000
--- a/gn/packages/opencl-icd-loader.scm
+++ /dev/null
@@ -1,46 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
-;;;
-;;; 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 (gn packages opencl-icd-loader)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix git-download)
-  #:use-module (guix download)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix packages)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages curl)
-  #:use-module (gnu packages boost)
-  #:use-module (gnu packages gawk)
-  #:use-module (gnu packages cmake)
-  #:use-module (gnu packages glib)
-  #:use-module (gnu packages image)
-  #:use-module (gnu packages video)
-  #:use-module (gnu packages textutils)
-  #:use-module (gnu packages gl)
-  #:use-module (gnu packages llvm)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages maths)
-  #:use-module (gnu packages mpi)
-  #:use-module (gnu packages web)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages xorg)
-  #:use-module (gnu packages version-control)  
-  #:use-module (gnu packages linux))
diff --git a/gn/packages/openfyba.scm b/gn/packages/openfyba.scm
deleted file mode 100644
index c1a1c90..0000000
--- a/gn/packages/openfyba.scm
+++ /dev/null
@@ -1,58 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
-;;; Copyright © 2019 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 (gn packages openfyba)
-  #:use-module ((guix licenses))
-  #:use-module (guix packages)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system gnu)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages gnupg))
-
-(define-public openfyba
-  (package
-   (name "openfyba")
-   (version "4.1.1")
-   (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                    (url "https://github.com/kartverket/fyba.git")
-                    (commit version)))
-             (file-name (git-file-name name version))
-             (sha256
-              (base32
-               "0zxw4pf3s7rb9g8209i3rj0v5jjw1vb79knd5mzvw9drpl9bbgpl"))))
-    (inputs `(("zip" ,zip)
-             ("autoconf" ,autoconf)
-             ("automake" ,automake)
-             ("libtool" ,libtool)
-             ("libgcrypt" ,libgcrypt)))
-    (build-system gnu-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'bootstrap
-           (lambda _
-             (for-each make-file-writable (find-files "." ".*"))
-             (invoke "autoreconf" "-vfi"))))))
-    (home-page "http://labs.kartverket.no/sos/")
-    (synopsis "source code release of the FYBA library")
-    (description "OpenFYBA is the source code release of the FYBA library.")
-    (license gpl2)))
diff --git a/gn/packages/static.scm b/gn/packages/static.scm
deleted file mode 100644
index 67b4873..0000000
--- a/gn/packages/static.scm
+++ /dev/null
@@ -1,83 +0,0 @@
-;;;
-;;; Commentary:
-;;;
-;;; This module contains statically linked executables meant for use
-;;; with spike and gem5.
-;;;
-
-;;;
-;;; Code:
-;;;
-
-(define-module (gn packages static)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages bioinformatics)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages cpp)
-  #:use-module (gnu packages jemalloc)
-  #:use-module (gnu packages maths)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix gexp)
-  #:use-module (guix packages)
-  #:use-module (guix utils))
-
-;; Static hello, for testing
-(define-public hello-static
-  (package
-    (inherit (static-package hello))
-    (name "hello-static")))
-
-;; A minimal version of htslib that does not depend on curl and openssl. This
-;; reduces the number of higher order dependencies in static linking.
-(define htslib-minimal
-  (package
-    (inherit htslib)
-    (arguments
-     (substitute-keyword-arguments (package-arguments htslib)
-       ((#:configure-flags flags ''())
-        ''())))
-    (inputs
-     (list bzip2 xz))))
-
-(define-public wfmash-static
-  (package
-    (inherit wfmash)
-    (name "wfmash-static")
-    (arguments
-     (substitute-keyword-arguments (package-arguments wfmash)
-       ((#:configure-flags flags ''())
-        `(cons* "-DCMAKE_EXE_LINKER_FLAGS=-static"
-                "-DCMAKE_SKIP_RPATH=TRUE"
-                ,flags))
-       ((#:phases phases ''())
-        #~(modify-phases #$phases
-            ;; When static linking, we need to link against the entire
-            ;; dependency tree, not just the direct first-order dependencies.
-            (add-after 'unpack 'add-higher-order-dependencies
-              (lambda _
-                (substitute* "CMakeLists.txt"
-                  (("hts" all)
-                   (string-append all " bz2 dl lzma"))
-                  (("jemalloc" all)
-                   ;; We add atomic because riscv64 has no lock-free atomic
-                   ;; instructions.
-                   (string-append all " atomic pthread")))))))))
-    (inputs
-     (list atomic-queue
-           (list gsl "static")
-           htslib-minimal
-           jemalloc
-           (list zlib "static")
-
-           ;; Second-order dependencies from htslib
-           (list bzip2 "static")
-           (list xz "static")))))
-
-(define-public smithwaterman-static
-  (package
-    (inherit smithwaterman)
-    (name "smithwaterman-static")
-    (arguments
-     (substitute-keyword-arguments (package-arguments smithwaterman)
-       ((#:make-flags flags ''())
-        #~(cons "CFLAGS=-static" #$flags))))))