[PATCH 0/2] gnu: Add EMBOSS.

[PATCH 0/2] gnu: Add EMBOSS.

[Ricardo Wurmus]

Hi Guix,

this patch set adds the bioinformatics package EMBOSS along with a PDF library
"libharu".

Ricardo Wurmus (2):
  gnu: Add libharu.
  gnu: Add EMBOSS.

 gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++
 gnu/packages/pdf.scm            | 42 +++++++++++++++++++++++++-
 2 files changed, 108 insertions(+), 1 deletion(-)

-- 
2.8.4

[PATCH 1/2] gnu: Add libharu.

[Ricardo Wurmus]

* gnu/packages/pdf.scm (libharu): New variable.
---
 gnu/packages/pdf.scm | 42 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index d46bd1f..36d3985 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2015, 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;;
@@ -28,6 +28,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages ghostscript)
@@ -154,6 +155,45 @@
 Poppler PDF rendering library.")
     (license license:lgpl2.1+)))
 
+(define-public libharu
+  (package
+   (name "libharu")
+   (version "2.3.0")
+   (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/libharu/libharu/archive/"
+                                 "RELEASE_"
+                                 (string-join (string-split version #\.) "_")
+                                 ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32
+               "1lm4v539y9cb1lvbq387j57sy7yxda3yv8b1pk8m6zazbp66i7lg"))))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags
+      (list (string-append "--with-zlib="
+                           (assoc-ref %build-inputs "zlib"))
+            (string-append "--with-png="
+                           (assoc-ref %build-inputs "libpng")))
+      #:phases
+      (modify-phases %standard-phases
+        (add-before 'configure 'autogen
+          (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+   (inputs
+    `(("zlib" ,zlib)
+      ("libpng" ,libpng)))
+   (native-inputs
+    `(("autoconf" ,autoconf)
+      ("automake" ,automake)
+      ("libtool" ,libtool)))
+   (home-page "http://libharu.org/")
+   (synopsis "Library for generating PDF files")
+   (description
+    "libHaru is a library for generating PDF files.  libHaru does not support
+reading and editing of existing PDF files.")
+   (license license:zlib)))
+
 (define-public xpdf
   (package
    (name "xpdf")
-- 
2.8.4

[PATCH 2/2] gnu: Add EMBOSS.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (emboss): New variable.
---
 gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 11784ab..05063d3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -49,6 +49,8 @@
   #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gd)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages machine-learning)
@@ -56,6 +58,7 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pcre)
+  #:use-module (gnu packages pdf)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
@@ -70,6 +73,7 @@
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
+  #:use-module (gnu packages xorg)
   #:use-module (gnu packages zip)
   #:use-module (srfi srfi-1))
 
@@ -5232,6 +5236,69 @@ datasets and the exploration of large datasets of genome
 intervals (e.g. genes, sequence alignments).")
       (license license:gpl2))))
 
+(define-public emboss
+  (package
+    (name "emboss")
+    (version "6.5.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
+                                  (version-major+minor version) ".0/"
+                                  "EMBOSS-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-hpdf="
+                            (assoc-ref %build-inputs "libharu")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-checks
+           (lambda _
+             ;; The PNGDRIVER tests check for the presence of libgd, libpng
+             ;; and zlib, but assume that they are all found at the same
+             ;; prefix.
+             (substitute* "configure.in"
+               (("CHECK_PNGDRIVER")
+                "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
+AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
+AM_CONDITIONAL(AMPNG, true)"))
+             #t))
+         (add-after 'unpack 'disable-update-check
+           (lambda _
+             ;; At build time there is no connection to the Internet, so
+             ;; looking for updates will not work.
+             (substitute* "Makefile.am"
+               (("\\$\\(bindir\\)/embossupdate") ""))
+             #t))
+         (add-before 'configure 'autogen
+           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+    (inputs
+     `(("perl" ,perl)
+       ("libpng" ,libpng)
+       ("gd" ,gd)
+       ("libx11" ,libx11)
+       ("libharu" ,libharu)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://emboss.sourceforge.net")
+    (synopsis "Molecular biology analysis suite")
+    (description "EMBOSS is the \"European Molecular Biology Open Software
+Suite\".  EMBOSS is an analysis package specially developed for the needs of
+the molecular biology (e.g. EMBnet) user community.  The software
+automatically copes with data in a variety of formats and even allows
+transparent retrieval of sequence data from the web.  It also provides a
+number of libraries for the development of software in the field of molecular
+biology.  EMBOSS also integrates a range of currently available packages and
+tools for sequence analysis into a seamless whole.")
+    (license license:gpl2+)))
+
 (define-public piranha
   ;; There is no release tarball for the latest version.  The latest commit is
   ;; older than one year at the time of this writing.
-- 
2.8.4

Re: [PATCH 0/2] gnu: Add EMBOSS.

[Roel Janssen]

Hello Ricardo,

Wow this is cool.  I thought EMBOSS had a lot more dependencies than
described in the provided patches.  This looks very clean.  Nice work :)

Kind regards,
Roel Janssen


Ricardo Wurmus writes:

> Hi Guix,
>
> this patch set adds the bioinformatics package EMBOSS along with a PDF library
> "libharu".
>
> Ricardo Wurmus (2):
>   gnu: Add libharu.
>   gnu: Add EMBOSS.
>
>  gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++
>  gnu/packages/pdf.scm            | 42 +++++++++++++++++++++++++-
>  2 files changed, 108 insertions(+), 1 deletion(-)

Re: [PATCH 1/2] gnu: Add libharu.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> * gnu/packages/pdf.scm (libharu): New variable.

LGTM, thanks!

Ludo’.

Re: [PATCH 2/2] gnu: Add EMBOSS.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> * gnu/packages/bioinformatics.scm (emboss): New variable.

I second Roel, this looks good to me.

Thank you!

Ludo’.

Re: [PATCH 2/2] gnu: Add EMBOSS.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> * gnu/packages/bioinformatics.scm (emboss): New variable.
>
> I second Roel, this looks good to me.

Thanks, I pushe this along with libharu.

~~ Ricardo