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authorpjotrp2016-12-11 05:28:40 +0000
committerpjotrp2016-12-11 05:28:40 +0000
commit0845b5345e84d0c3000cdeee3b4c42b17b85ddf0 (patch)
tree07e6b022b09c161f16c50c43fc061e47c7f41059
parentead155ea6347141ffb1279aefb35f5faccff5047 (diff)
parentc3031134beda3f1951742a6d4ca05c85f034af49 (diff)
downloadguix-bioinformatics-0845b5345e84d0c3000cdeee3b4c42b17b85ddf0.tar.gz
Merge branch 'master' of github.com:genenetwork/guix-bioinformatics into gn-deploy
-rw-r--r--gn/packages/ldc.scm322
-rw-r--r--gn/packages/ruby.scm120
2 files changed, 442 insertions, 0 deletions
diff --git a/gn/packages/ldc.scm b/gn/packages/ldc.scm
new file mode 100644
index 0000000..45ba1b4
--- /dev/null
+++ b/gn/packages/ldc.scm
@@ -0,0 +1,322 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015, 2016 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
+;;;
+;;; 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 ldc)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix packages)
+ #:use-module (guix download)
+ #:use-module (guix git-download)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix build-system cmake)
+ #:use-module (gnu packages)
+ #:use-module (gnu packages base)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages libedit)
+ #:use-module (gnu packages llvm)
+ #:use-module (gnu packages textutils)
+ #:use-module (gnu packages zip))
+
+(define-public rdmd
+ (let ((commit "da0a2e0a379b08294015eec9d531f1e5dd4226f0"))
+ (package
+ (name "rdmd")
+ (version (string-append "v2.070.0-1." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/D-Programming-Language/tools.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check) ; There is no Makefile, so there's no 'make check'.
+ (replace
+ 'build
+ (lambda _
+ (zero? (system* "ldc2" "rdmd.d"))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "rdmd" bin)))))))
+ (native-inputs
+ `(("ldc" ,ldc)))
+ (home-page "https://github.com/D-Programming-Language/tools/")
+ (synopsis "Specialized equivalent to 'make' for the D language")
+ (description
+ "rdmd is a companion to the dmd compiler that simplifies the typical
+edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like
+make and other tools, rdmd uses the relative dates of the files involved to
+minimize the amount of work necessary. Unlike make, rdmd tracks dependencies
+and freshness without requiring additional information from the user.")
+ (license license:boost1.0))))
+
+(define-public ldc-0.16.1
+ (package
+ (name "ldc")
+ (version "0.16.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/ldc/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1jvilxx0rpqmkbja4m69fhd5g09697xq7vyqp2hz4hvxmmmv4j40"))))
+ (build-system cmake-build-system)
+ ;; LDC currently only supports the x86_64 and i686 architectures.
+ (supported-systems '("x86_64-linux" "i686-linux"))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (zero? (system* "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and (unpack "phobos-src" "runtime/phobos")
+ (unpack "druntime-src" "runtime/druntime")
+ (unpack "dmd-testsuite-src" "tests/d2/dmd-testsuite")))))
+ (add-after 'unpack-submodule-sources 'patch-dmd2
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "dmd2/root/port.c"
+ ((" ::isnan") " isnan")
+ ((" ::isinf") " isinf")
+ (("#undef isnan") "")
+ (("#undef isinf") ""))
+ #t))
+ (add-after 'unpack-submodule-sources 'patch-phobos
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "runtime/phobos/std/process.d"
+ (("/bin/sh") (which "sh"))
+ (("echo") (which "echo")))
+ (substitute* "runtime/phobos/std/datetime.d"
+ (("/usr/share/zoneinfo/")
+ (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")))
+ (substitute* "tests/d2/dmd-testsuite/Makefile"
+ (("/bin/bash") (which "bash")))
+ #t)))))
+ (inputs
+ `(("libconfig" ,libconfig)
+ ("libedit" ,libedit)
+ ("tzdata" ,tzdata)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("llvm" ,llvm-3.7)
+ ("clang" ,clang-3.7)
+ ("unzip" ,unzip)
+ ("phobos-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/phobos/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0sgdj0536c4nb118yiw1f8lqy5d3g3lpg9l99l165lk9xy45l9z4"))
+ (patches (search-patches "ldc-disable-tests.patch"))))
+ ("druntime-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/druntime/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0z4mkyddx6c4sy1vqgqvavz55083dsxws681qkh93jh1rpby9yg6"))))
+ ("dmd-testsuite-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0yc6miidzgl9k33ygk7xcppmfd6kivqj02cvv4fmkbs3qz4yy3z1"))))))
+ (home-page "http://wiki.dlang.org/LDC")
+ (synopsis "LLVM compiler for the D programming language")
+ (description
+ "LDC is a compiler for the D programming language. It is based on the
+latest DMD frontend and uses LLVM as backend.")
+ ;; Most of the code is released under BSD-3, except for code originally
+ ;; written for GDC, which is released under GPLv2+, and the DMD frontend,
+ ;; which is released under the "Boost Software License version 1.0".
+ (license (list license:bsd-3
+ license:gpl2+
+ license:boost1.0))))
+
+(define-public ldc-0.17.2
+ (package
+ (inherit ldc)
+ (name "ldc")
+ (version "0.17.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/ldc/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0iksl6cvhsiwnlh15b7s9v8f3grxk27jn0vja9n4sad7fvfwmmlc"))))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (zero? (system* "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and (unpack "phobos-src" "runtime/phobos")
+ (unpack "druntime-src" "runtime/druntime")
+ (unpack "dmd-testsuite-src" "tests/d2/dmd-testsuite")))))
+ (add-after 'unpack-submodule-sources 'patch-dmd2
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "dmd2/root/port.c"
+ ((" ::isnan") " isnan")
+ ((" ::isinf") " isinf")
+ (("#undef isnan") "")
+ (("#undef isinf") ""))
+ #t))
+ (add-after 'unpack-submodule-sources 'patch-phobos
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "runtime/phobos/std/process.d"
+ (("/bin/sh") (which "sh"))
+ (("echo") (which "echo")))
+ (substitute* "runtime/phobos/std/datetime.d"
+ (("/usr/share/zoneinfo/")
+ (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")))
+ (substitute* "tests/d2/dmd-testsuite/Makefile"
+ (("/bin/bash") (which "bash")))
+ #t)))
+ #:tests? #f))
+ (native-inputs
+ `(("llvm" ,llvm-3.7)
+ ("clang" ,clang-3.7)
+ ("unzip" ,unzip)
+ ("phobos-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/phobos/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "07hh3ic3r755mq9hn9gfr0wlc5y8cr91xz2ydb6gqy4zy8jgp5s9"))))
+ ("druntime-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/druntime/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1m1dhday9dl3s04njmd29z7ism2xn2ksb9qlrwzykdgz27b3dk6x"))))
+ ("dmd-testsuite-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0n7gvalxwfmia4gag53r9qhcnk2cqrw3n4icj1yri0zkgc27pm60"))))))))
+
+(define-public ldc-1.1.0-beta4
+ (package
+ (inherit ldc)
+ (name "ldc")
+ (version "1.1.0-beta4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/ldc/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "04n6sbz6l658s32f7zilpbi9m8a1m4g5wrgl44igkvla30niy5yn"))))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (zero? (system* "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and (unpack "phobos-src" "runtime/phobos")
+ (unpack "druntime-src" "runtime/druntime")
+ (unpack "dmd-testsuite-src" "tests/d2/dmd-testsuite")))))
+ (add-after 'unpack-submodule-sources 'patch-phobos
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "runtime/phobos/std/process.d"
+ (("/bin/sh") (which "sh"))
+ (("echo") (which "echo")))
+ (substitute* "runtime/phobos/std/datetime.d"
+ (("/usr/share/zoneinfo/")
+ (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")))
+ (substitute* "tests/d2/dmd-testsuite/Makefile"
+ (("/bin/bash") (which "bash")))
+ #t)))
+ #:tests? #f))
+ (native-inputs
+ `(("llvm" ,llvm-3.7)
+ ("ldc" ,ldc-0.17.2)
+ ("phobos-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/phobos/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1iwy5rs0rqkicj1zfsa5yqvk8ard99bfr8g69qmhlbzb98q0kpks"))))
+ ("druntime-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/druntime/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1qsiw5lz1pr8ms9myjf8b94nqi7f1781k226jvxwnhkjg11d0s63"))))
+ ("dmd-testsuite-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0jp54hyi75i9g41rvgmm3zg21yzv57q8dghrhb432rb0n9j15mbp"))))))))
+
+(define-public ldc ldc-1.1.0-beta4)
diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm
index 93f4628..41743d9 100644
--- a/gn/packages/ruby.scm
+++ b/gn/packages/ruby.scm
@@ -149,3 +149,123 @@ output")
(home-page
"http://github.com/pjotrp/bioruby-table")
(license expat)))
+
+(define-public ruby-net-http-digest-auth
+ (package
+ (name "ruby-net-http-digest-auth")
+ (version "1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "net-http-digest_auth" version))
+ (sha256
+ (base32
+ "14801gr34g0rmqz9pv4rkfa3crfdbyfk6r48vpg5a5407v0sixqi"))))
+ (build-system ruby-build-system)
+ (arguments
+ `(#:tests? #f))
+ (synopsis
+ "An implementation of RFC 2617 - Digest Access Authentication. At this time
+the gem does not drop in to Net::HTTP and can be used for with other HTTP
+clients.
+
+In order to use net-http-digest_auth you'll need to perform some request
+wrangling on your own. See the class documentation at Net::HTTP::DigestAuth
+for an example.")
+ (description
+ "An implementation of RFC 2617 - Digest Access Authentication. At this time
+the gem does not drop in to Net::HTTP and can be used for with other HTTP
+clients.
+
+In order to use net-http-digest_auth you'll need to perform some request
+wrangling on your own. See the class documentation at Net::HTTP::DigestAuth
+for an example.")
+ (home-page
+ "http://github.com/drbrain/net-http-digest_auth")
+ (license #f)))
+
+(define-public ruby-ntlm-http
+ (package
+ (name "ruby-ntlm-http")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "ntlm-http" version))
+ (sha256
+ (base32
+ "0yx01ffrw87wya1syivqzf8hz02axk7jdpw6aw221xwvib767d36"))))
+ (build-system ruby-build-system)
+ (arguments
+ `(#:tests? #f))
+ (synopsis
+ "Ruby/NTLM HTTP provides NTLM authentication over http.")
+ (description
+ "Ruby/NTLM HTTP provides NTLM authentication over http.")
+ (home-page "http://www.mindflowsolutions.net")
+ (license #f)))
+
+(define-public ruby-webrobots
+ (package
+ (name "ruby-webrobots")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "webrobots" version))
+ (sha256
+ (base32
+ "19ndcbba8s8m62hhxxfwn83nax34rg2k5x066awa23wknhnamg7b"))))
+ (build-system ruby-build-system)
+ (arguments
+ `(#:tests? #f))
+ (synopsis
+ "This library helps write robots.txt compliant web robots in Ruby.
+")
+ (description
+ "This library helps write robots.txt compliant web robots in Ruby.
+")
+ (home-page "https://github.com/knu/webrobots")
+ (license #f)))
+
+(define-public ruby-mechanize
+ (package
+ (name "ruby-mechanize")
+ (version "2.7.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "mechanize" version))
+ (sha256
+ (base32
+ "1f861x62kmggy60krv229s5jl7afq9nblwcfih3kp9bm5c5jn16y"))))
+ (build-system ruby-build-system)
+ (arguments '(#:gem-flags '("--trace")))
+ (inputs
+ `(("ruby" ,ruby)))
+ (propagated-inputs
+ `(("ruby-domain-name" ,ruby-domain-name)
+ ("ruby-http-cookie" ,ruby-http-cookie)
+ ("ruby-mime-types" ,ruby-mime-types)
+ ("ruby-net-http-digest-auth"
+ ,ruby-net-http-digest-auth)
+ ("ruby-net-http-persistent"
+ ,ruby-net-http-persistent)
+ ("ruby-nokogiri" ,ruby-nokogiri)
+ ("ruby-ntlm-http" ,ruby-ntlm-http)
+ ("ruby-webrobots" ,ruby-webrobots)))
+ (synopsis
+ "The Mechanize library is used for automating interaction with websites.
+Mechanize automatically stores and sends cookies, follows redirects,
+and can follow links and submit forms. Form fields can be populated and
+submitted. Mechanize also keeps track of the sites that you have visited as
+a history.")
+ (description
+ "The Mechanize library is used for automating interaction with websites.
+Mechanize automatically stores and sends cookies, follows redirects,
+and can follow links and submit forms. Form fields can be populated and
+submitted. Mechanize also keeps track of the sites that you have visited as
+a history.")
+ (home-page
+ "http://docs.seattlerb.org/mechanize/")
+ (license expat)))