Merge branch 'master' of https://github.com/genenetwork/guix-bioinformatics

3 files changed, 110 insertions, 109 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1f6052e..68095e9 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -78,7 +78,7 @@
     (propagated-inputs
      `(("python" ,python-2)
        ("r" ,r)
-       ("r-dnacopy" ,r-dnacopy)
+       ;; ("r-dnacopy" ,r-dnacopy) <-- missing in Pjotr's tree
        ("bedtools" ,bedtools)
        ("samtools" ,samtools)))
     (arguments
@@ -1049,56 +1049,6 @@ subset of samtools functionality, including view, index, sort,
 markdup, and depth.")
       (license license:gpl2+))))
 
-(define-public picard
-  (package
-    (name "picard")
-    (version "2.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/broadinstitute/picard/archive/"
-             version ".tar.gz"))
-       (sha256
-        (base32 ""))))
-    (build-system gnu-build-system)
-    (home-page "http://broadinstitute.github.io/picard/")
-    (synopsis "A set of Java command line tools for manipulating high-throughput
-sequencing data (HTS) data and formats")
-    (description "Picard comprises Java-based command-line utilities that
-manipulate SAM files, and a Java API (HTSJDK) for creating new programs that
-read and write SAM files. Both SAM text format and SAM binary (BAM) format are
-supported.")
-    ;; The license is MIT.
-    (license license:expat)
-))
-
-(define-public fastqc
-  (package
-    (name "fastqc")
-    (version "0.11.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"
-             version "_source.zip"))
-       (sha256
-        (base32 ""))))
-    (build-system gnu-build-system)
-    (arguments
-     `(("perl" ,perl) ; Needed to run the java command.
-       ("jdk" ,icedtea "jdk")))
-    (native-inputs
-     `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK..
-       ("jdk" ,icedtea "jdk")
-       ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy.
-       ("unzip" ,unzip)))
-    (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
-    (synopsis "A quality control tool for high throughput sequence data")
-    (description
-     "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.")
-    (license license:gpl3+)))
 
 (define-public vcflib
   (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
diff --git a/gn/packages/elixir.scm b/gn/packages/elixir.scm
new file mode 100644
index 0000000..2f9bcc3
--- /dev/null
+++ b/gn/packages/elixir.scm
@@ -0,0 +1,67 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;;
+;;; 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 elixir)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gn packages erlang)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages tls))
+
+(define-public elixir
+  (package
+    (name "elixir")
+    (version "1.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/elixir-lang/elixir/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "09s8469830s4070i0m04fxdhqimkdyc5k9jylm5vpfz9l3z4wvl8"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("erlang" ,erlang)))
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before
+          'build 'rewrite-path
+          (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "bin/elixir"
+                     (("ERL_EXEC=\"erl\"") (string-append "ERL_EXEC=" (which "erl"))))))                           
+        ;; (replace 'check
+        ;;          (lambda _
+        ;;           (zero? (system* "make" "test")))))))
+        )
+       #:make-flags (list (string-append "PREFIX=" %output))
+       #:tests? #f)) ;; 2845 tests, 12 failures
+    (home-page "http://elixir-lang.org/")
+    (synopsis "The Elixir programming language")
+(description "Elixir is a dynamic, functional language designed for
+building scalable and maintainable applications. Elixir leverages the
+Erlang VM, known for running low-latency, distributed and
+fault-tolerant systems, while also being successfully used in web
+development and the embedded software domain.")
+    (license license:asl2.0)))
diff --git a/gn/packages/erlang.scm b/gn/packages/erlang.scm
index ebf98cf..117057b 100644
--- a/gn/packages/erlang.scm
+++ b/gn/packages/erlang.scm
@@ -22,17 +22,14 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system trivial)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages compression)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages tls))
 
 (define-public erlang
-  ;; Keep in sync with 'erlang-manpages'!
   (package
     (name "erlang")
+    ;; When updating, remember to update the hash of erlang-manpages!
     (version "18.3")
     (source (origin
               (method url-fetch)
@@ -45,7 +42,17 @@
                 "1hy9slq9gjvwdb504dmvp6rax90isnky6chqkyq5v4ybl4lq3azx"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("perl" ,perl)))
+     `(("perl" ,perl)
+
+       ;; Erlang's documentation is distributed in a separate tarball.
+       ("erlang-manpages"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "http://erlang.org/download/otp_doc_man_"
+                               version ".tar.gz"))
+           (sha256
+            (base32
+             "1hpcr7a3dx2y9gnb53bvb4g6lyvbwigadl9s3f978s01x40f32wp"))))))
     (inputs
      `(("ncurses" ,ncurses)
        ("openssl" ,openssl)))
@@ -54,28 +61,28 @@
        (list (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl")))
        #:phases
        (modify-phases %standard-phases
-	 (add-after 'patch-source-shebangs 'patch-source-env
-	   (lambda _
-	     (let ((escripts
-		    (append
-		     (find-files "." "\\.escript")
-		     (find-files "lib/stdlib/test/escript_SUITE_data/")
-		     '("erts/lib_src/utils/make_atomics_api"
-		       "erts/preloaded/src/add_abstract_code"
-		       "lib/diameter/bin/diameterc"
-		       "lib/reltool/examples/display_args"
-		       "lib/reltool/examples/mnesia_core_dump_viewer"
-		       "lib/snmp/src/compile/snmpc.src"
-		       "make/verify_runtime_dependencies"
-		       "make/emd2exml.in"))))
-	       (substitute* escripts
-		 (("/usr/bin/env") (which "env"))))))
          (add-after 'unpack 'path-to-rm
            (lambda _
              (substitute* "erts/configure"
                (("/bin/rm") (which "rm")))
              (substitute* "lib/odbc/configure"
                (("/bin/rm") (which "rm")))))
+         (add-after 'patch-source-shebangs 'patch-source-env
+           (lambda _
+             (let ((escripts
+                    (append
+                     (find-files "." "\\.escript")
+                     (find-files "lib/stdlib/test/escript_SUITE_data/")
+                     '("erts/lib_src/utils/make_atomics_api"
+                       "erts/preloaded/src/add_abstract_code"
+                       "lib/diameter/bin/diameterc"
+                       "lib/reltool/examples/display_args"
+                       "lib/reltool/examples/mnesia_core_dump_viewer"
+                       "lib/snmp/src/compile/snmpc.src"
+                       "make/verify_runtime_dependencies"
+                       "make/emd2exml.in"))))
+               (substitute* escripts
+                 (("/usr/bin/env") (which "env"))))))
          (add-before 'configure 'set-erl-top
            (lambda _
              (setenv "ERL_TOP" (getcwd))))
@@ -83,7 +90,20 @@
            ;; This only works after install.
            (lambda _
              (substitute* (string-append (assoc-ref %outputs "out") "/bin/erl")
-               (("sed") (which "sed"))))))
+               (("sed") (which "sed")))))
+         (add-after 'install 'install-doc
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (manpages (assoc-ref inputs "erlang-manpages"))
+                    (share (string-append out "/share/")))
+             (mkdir-p share)
+             (with-directory-excursion share
+               (and
+                 (zero? (system* "tar" "xvf" manpages))
+                 ;; Delete superfluous files.
+                 (for-each delete-file '("COPYRIGHT"
+                                         "PR.template"
+                                         "README"))))))))
        #:test-target "release_tests"))
     (home-page "http://erlang.org/")
     (synopsis "The Erlang programming language")
@@ -94,39 +114,3 @@ availability.  Some of its uses are in telecoms, banking, e-commerce,
 computer telephony and instant messaging.  Erlang's runtime system has
 built-in support for concurrency, distribution and fault tolerance.")
     (license license:asl2.0)))
-
-(define-public erlang-manpages
-  ;; Keep in sync with 'erlang'!
-  (package
-    (name "erlang-manpages")
-    (version (package-version erlang))
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://erlang.org/download/otp_doc_man_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "1hpcr7a3dx2y9gnb53bvb4g6lyvbwigadl9s3f978s01x40f32wp"))))
-    (build-system trivial-build-system)
-    (arguments
-     '(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         (let* ((gz  (assoc-ref %build-inputs "gzip"))
-                (tar (assoc-ref %build-inputs "tar"))
-                (out (assoc-ref %outputs "out"))
-                (man (string-append out "/share/man")))
-           (setenv "PATH" (string-append tar "/bin:" gz "/bin"))
-           (mkdir-p man)
-           (with-directory-excursion man
-             (zero? (system* "tar" "xvf"
-                             (assoc-ref %build-inputs "source"))))
-           (delete-file (string-append man "/PR.template"))
-           (delete-file (string-append man "/README"))))))
-    (native-inputs `(("tar" ,tar)
-                     ("gzip" ,gzip)))
-    (synopsis "Man pages of Erlang")
-    (description "This provides the man pages of Erlang.")
-    (home-page (package-home-page erlang))
-    (license license:asl2.0)))