Merge branch 'master' of github.com:genenetwork/guix-bioinformatics into gn-deploy

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)))