PATCH [0/22]: Add roary.

PATCH [0/22]: Add roary.

[Ben Woodcroft]

Hi all,

This patchset adds roary, a pipeline which at times is used for tracking
outbreaks of pathogenic bacteria in e.g. foodstuffs or hospitals, by comparing
whole genome sequences.

perl-log-log4perl was already discussed previously and I am happy to
defer to that patch.  I only include mine here so the packages build.
https://lists.gnu.org/archive/html/guix-devel/2016-07/msg00624.html

Thanks for any review in advance.
ben

[PATCH 01/22] gnu: parallel: Use full paths for executables.

[Ben Woodcroft]

* gnu/packages/parallel.scm (parallel)[inputs]: Add procps.
[arguments]: New field.
---
 gnu/packages/parallel.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 12f0028..3bb078e 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -54,7 +55,31 @@
        (base32
         "08gm0i9vj2nz8qgqi98z00myypgb3dni0s5yf3l17fp8h78fp4g3"))))
     (build-system gnu-build-system)
-    (inputs `(("perl" ,perl)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-bin-sh
+           (lambda _
+             (for-each
+              (lambda (file)
+                (substitute* file
+                  ;; Patch hard coded '/bin/sh' in the lin ending in:
+                  ;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
+                  ;;  parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
+                  (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))
+                  ;; Patch call to 'ps' and 'perl' commands.
+                  ((" ps ") (string-append " " (which "ps") " "))
+                  ((" perl -") (string-append " " (which "perl") " -"))))
+              (list "src/parallel" "src/sem"))))
+         (add-after 'install 'post-install-test
+           (lambda* (#:key outputs #:allow-other-keys)
+             (zero? (system* (string-append
+                              (assoc-ref outputs "out") "/bin/parallel")
+                             "echo"
+                             ":::" "1" "2" "3")))))))
+    (inputs
+     `(("perl" ,perl)
+       ("procps" ,procps)))
     (home-page "http://www.gnu.org/software/parallel/")
     (synopsis "Build and execute command lines in parallel")
     (description
-- 
2.9.1

[PATCH 02/22] gnu: Add perl-xml-writer.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-xml-writer): New variable.
---
 gnu/packages/perl.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index f42abee..844178a 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -10,6 +10,7 @@
 ;;; Coypright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -6416,6 +6417,33 @@ it.  With this module, you can add your own magic to any variable without
 having to write a single line of XS.")
     (license (package-license perl))))
 
+(define-public perl-xml-writer
+  (package
+    (name "perl-xml-writer")
+    (version "0.625")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/J/JO/JOSEPHW/XML-Writer-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1gjzs570i67ywbv967g8ylb5sg59clwmyrl2yix3jl70dhn55070"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/XML-Writer")
+    (synopsis "Easily generate well-formed, namespace-aware XML")
+    (description "@code{XML::Writer} is a simple Perl module for writing XML
+documents: it takes care of constructing markup and escaping data correctly.
+By default, it also performs a significant amount of well-formedness checking
+on the output to make certain (for example) that start and end tags match,
+that there is exactly one document element, and that there are not duplicate
+attribute names.")
+    ;; Redistribution and use in source and compiled forms, with or without
+    ;; modification, are permitted under any circumstances.  No warranty.
+    (license public-domain)))
+
 (define-public perl-yaml
   (package
     (name "perl-yaml")
-- 
2.9.1

[PATCH 03/22] gnu: Add perl-parse-yapp.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-parse-yapp): New variable.
---
 gnu/packages/perl.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 844178a..76eeee3 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -6490,6 +6490,27 @@ YAML-style files, written with as little code as possible, reducing load time
 and memory overhead.")
     (license (package-license perl))))
 
+(define-public perl-parse-yapp
+  (package
+    (name "perl-parse-yapp")
+    (version "1.05")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/F/FD/FDESAR/Parse-Yapp-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0azjqqf4m7nkfgmmj4q77vy9sdgg01wn8xxv40bq3pis93xnr2i2"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/Parse-Yapp")
+    (synopsis "Generate and use LALR parsers")
+    (description "This package compiles yacc-like @dfn{Look Ahead LR} (LALR)
+grammars to generate Perl object oriented parser modules.")
+    (license (package-license perl))))
+
 \f
 ;;; Some packaged modules need versions of core modules that are newer than
 ;;; those in our perl 5.16.1.
-- 
2.9.1

[PATCH 04/22] gnu: Add perl-graph.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-graph): New variable.
---
 gnu/packages/perl.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 76eeee3..891e1a9 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2532,6 +2532,27 @@ vaguely inspired by John Ousterhout's Tk_ParseArgv.")
                               "Getopt-Tabular-" version))
     (license (package-license perl))))
 
+(define-public perl-graph
+  (package
+    (name "perl-graph")
+    (version "0.9704")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/J/JH/JHI/Graph-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "099a1gca0wj5zs0cffncjqp2mjrdlk9i6325ks89ml72gfq8wpij"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/Graph")
+    (synopsis "Graph data structures and algorithms")
+    (description "This is @code{Graph}, a Perl module for dealing with graphs,
+the abstract data structures.")
+    (license (package-license perl))))
+
 (define-public perl-guard
   (package
     (name "perl-guard")
-- 
2.9.1

[PATCH 05/22] gnu: Add perl-graph-readwrite.

[Ben Woodcroft]

* gnu/packages/xml.scm (perl-graph-readwrite): New variable.
---
 gnu/packages/xml.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index af597b8..0533cb9 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Raimon Grau <raimonster@gmail.com>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -188,6 +189,38 @@ based on libxml for XML parsing, tree manipulation and XPath support.")
           (base32
            "1klh81xbm9ppzgqk339097i39b7fnpmlj8lzn8bpczl3aww6x5xm")))))))
 
+(define-public perl-graph-readwrite
+  (package
+    (name "perl-graph-readwrite")
+    (version "2.08")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/N/NE/NEILB/Graph-ReadWrite-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1wjni212nfz9irp19nx9if1lj3w9cybpdbzhii4g8macpryjj7ci"))))
+    (build-system perl-build-system)
+    (propagated-inputs
+     `(("perl-graph" ,perl-graph)
+       ("perl-parse-yapp" ,perl-parse-yapp)
+       ("perl-xml-parser" ,perl-xml-parser)
+       ("perl-xml-writer" ,perl-xml-writer)))
+    (home-page "http://search.cpan.org/dist/Graph-ReadWrite")
+    (synopsis "Modules for reading and writing directed graphs")
+    (description "This is a collection of perl classes for reading and writing
+directed graphs in a variety of file formats.  The graphs are represented in
+Perl using Jarkko Hietaniemi's @code{Graph} classes.
+
+There are two base classes. @code{Graph::Reader} is the base class for classes
+which read a graph file and create an instance of the Graph class.
+@code{Graph::Writer} is the base class for classes which take an instance of
+the @code{Graph} class and write it out in a specific file format.")
+    (license (package-license perl))))
+
 (define-public perl-xml-parser
   (package
     (name "perl-xml-parser")
-- 
2.9.1

[PATCH 06/22] gnu: Add perl-log-log4perl.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-log-log4perl): New variable.
---
 gnu/packages/perl.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 891e1a9..d37a1a3 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2961,6 +2961,28 @@ either uses the first module it finds or throws an error.")
 versa.")
     (license (package-license perl))))
 
+(define-public perl-log-log4perl
+  (package
+    (name "perl-log-log4perl")
+    (version "1.47")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/M/MS/MSCHILLI/Log-Log4perl-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0vxraq9navx5mgf8y8g6l5rbl3dv2ml8bishka5m69hj07nxs0ch"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/Log-Log4perl")
+    (synopsis "Log4j implementation for Perl")
+    (description "@code{Log::Log4perl} lets you remote-control and fine-tune
+the logging behaviour of your system from the outside.  It implements the
+widely popular (Java-based) Log4j logging package in pure Perl.")
+    (license (package-license perl))))
+
 (define-public perl-log-report-optional
   (package
     (name "perl-log-report-optional")
-- 
2.9.1

[PATCH 07/22] gnu: Add perl-file-slurper.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-file-slurper): New variable.
---
 gnu/packages/perl.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index d37a1a3..6a7b02d 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2404,6 +2404,29 @@ files with a simple call.  It also has a subroutine for reading the list of
 file names in a directory.")
     (license (package-license perl))))
 
+(define-public perl-file-slurper
+  (package
+    (name "perl-file-slurper")
+    (version "0.008")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/L/LE/LEONT/File-Slurper-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0cyjspspms6zyjcqz9v18dbs574g085h2jzjh41xvsrc1qa8bxhh"))))
+    (build-system perl-build-system)
+    (propagated-inputs
+     `(("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)))
+    (home-page "http://search.cpan.org/dist/File-Slurper")
+    (synopsis "Simple, sane and efficient module to slurp a file")
+    (description "This module provides functions for fast and correct file
+slurping and spewing.  All functions are optionally exported.")
+    (license (package-license perl))))
+
 (define-public perl-file-slurp-tiny
   (package
     (name "perl-file-slurp-tiny")
-- 
2.9.1

[PATCH 08/22] gnu: Add perl-file-path.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-file-path): New variable.
---
 gnu/packages/perl.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 6a7b02d..f19ddc0 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2287,6 +2287,28 @@ that arise trying to find them consistently across a wide variety of
 platforms.")
     (license (package-license perl))))
 
+(define-public perl-file-path
+  (package
+    (name "perl-file-path")
+    (version "2.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/R/RI/RICHE/File-Path-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0znihrlcnlpa0ziml0hkq9s59p1bjd2a6khgx2accdf16w6imxmv"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/File-Path")
+    (synopsis "Create or remove directory trees")
+    (description "This module provide a convenient way to create directories
+of arbitrary depth and to delete an entire directory subtree from the
+filesystem.")
+    (license (package-license perl))))
+
 (define-public perl-file-list
   (package
     (name "perl-file-list")
-- 
2.9.1

[PATCH 09/22] gnu: Add perl-file-grep.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-file-grep): New variable.
---
 gnu/packages/perl.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index f19ddc0..4d7cab3 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2262,6 +2262,29 @@ types Perl-related files, or replicating search queries run on a distribution
 in various parts of the CPAN ecosystem.")
     (license (package-license perl))))
 
+(define-public perl-file-grep
+  (package
+    (name "perl-file-grep")
+    (version "0.02")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/M/MN/MNEYLON/File-Grep-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0cjnz3ak7s3x3y3q48xb9ka2q9d7xvch58vy80hqa9xn9qkiabj6"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/File-Grep")
+    (synopsis "Matches patterns in a series of files")
+    (description "@code{File::Grep} provides similar functionality as perl's
+builtin @code{grep}, @code{map}, and @code{foreach} commands, but iterating
+over a passed filelist instead of arrays.  While trivial, this module can
+provide a quick dropin when such functionality is needed.")
+    (license (package-license perl))))
+
 (define-public perl-file-homedir
   (package
     (name "perl-file-homedir")
-- 
2.9.1

[PATCH 10/22] gnu: Add perl-array-utils.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-array-utils): New variable.
---
 gnu/packages/perl.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 4d7cab3..199b2ee 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -225,6 +225,27 @@ manipulate, read, and write Zip archive files.")
     (home-page "http://search.cpan.org/~phred/Archive-Zip-1.37/lib/Archive/Zip.pm")
     (license (package-license perl))))
 
+(define-public perl-array-utils
+  (package
+    (name "perl-array-utils")
+    (version "0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/Z/ZM/ZMIJ/Array/Array-Utils-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0w1pwvnjdpb0n6k07zbknxwx6v7y75p4jxrs594pjhwvrmzippc9"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/Array-Utils")
+    (synopsis "Small utils for array manipulation")
+    (description "@code{Array::Utils} is a small pure-perl module containing
+list manipulation routines.")
+    (license (package-license perl))))
+
 (define-public perl-base
   (package
     (name "perl-base")
-- 
2.9.1

[PATCH 11/22] gnu: Add perl-test-files.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-test-files): New variable.
---
 gnu/packages/perl.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 199b2ee..590ddf4 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -5486,6 +5486,31 @@ Test::Exception.  It does much less, but should allow greater flexibility in
 testing exception-throwing code with about the same amount of typing.")
     (license (package-license perl))))
 
+(define-public perl-test-files
+  (package
+    (name "perl-test-files")
+    (version "0.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/P/PH/PHILCROW/Test-Files-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1zn33yigznq7i1jr4yjr4lxvc6bn7znkbqdzj7slhc146pqapkln"))))
+    (build-system perl-build-system)
+    (propagated-inputs
+     `(("perl-algorithm-diff" ,perl-algorithm-diff)
+       ("perl-text-diff" ,perl-text-diff)))
+    (home-page "http://search.cpan.org/dist/Test-Files")
+    (synopsis "Ease software testing with files and directories")
+    (description "This library provides functions to enable testing of files
+and directories.  For instance, the @code{file_ok} helper can test whether the
+contents of a file is equal to a particular string.")
+    (license (package-license perl))))
+
 (define-public perl-test-harness
   (package
     (name "perl-test-harness")
-- 
2.9.1

[PATCH 12/22] gnu: Add perl-env-path.

[Ben Woodcroft]

* gnu/packages/perl.scm (perl-env-path): New variable.
---
 gnu/packages/perl.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 590ddf4..cbd3ef8 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2008,6 +2008,29 @@ SHA-1 message digest algorithm for use by Perl programs.")
 modules separately and deal with them after the module is done installing.")
     (license (package-license perl))))
 
+(define-public perl-env-path
+  (package
+    (name "perl-env-path")
+    (version "0.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/D/DS/DSB/Env-Path-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1qhmj15a66h90pjl2dgnxsb9jj3b1r5mpvnr87cafcl8g69z0jr4"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/Env-Path")
+    (synopsis "Advanced operations on path variables")
+    (description "@code{Env::Path} presents an object-oriented interface to
+path variables, defined as that subclass of environment variables which name
+an ordered list of filesystem elements separated by a platform-standard
+separator.")
+    (license (package-license perl))))
+
 (define-public perl-error
   (package
     (name "perl-error")
-- 
2.9.1

[PATCH 13/22] gnu: Add mcl.

[Ben Woodcroft]

* gnu/packages/machine-learning.scm (mcl): New variable.
---
 gnu/packages/machine-learning.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 2ccf0f2..3f2e502 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -33,6 +33,7 @@
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages statistics)
@@ -200,6 +201,32 @@ Markov Models} (HMM) and algorithms: discrete, continous emissions, basic
 training, HMM clustering, HMM mixtures.")
       (license license:lgpl2.0+))))
 
+(define-public mcl
+  (package
+    (name "mcl")
+    (version "14.137")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://micans.org/mcl/src/mcl-"
+                    (string-replace-substring version "." "-")
+                    ".tar.gz"))
+              (sha256
+               (base32
+                "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags (list "--enable-blast")))
+    (inputs
+     `(("perl" ,perl)))
+    (home-page "http://micans.org/mcl/")
+    (synopsis "Clustering algorithm for graphs")
+    (description
+     "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
+fast and scalable unsupervised cluster algorithm for graphs (also known as
+networks) based on simulation of (stochastic) flow in graphs.")
+    (license license:gpl3)))
+
 (define-public randomjungle
   (package
     (name "randomjungle")
-- 
2.9.1

Re: [PATCH 13/22] gnu: Add mcl.

[Leo Famulari]

On Wed, Jul 27, 2016 at 10:54:14PM +1000, Ben Woodcroft wrote:
> * gnu/packages/machine-learning.scm (mcl): New variable.

> +    (license license:gpl3)))

I skimmed the headers of some files in 'src/', and they say "or later".
Can you double-check if it should be gpl3+?

[PATCH 14/22] gnu: Add bpp-core.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (bpp-core): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6065a00..4fb23a4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -470,6 +470,39 @@ into separate processes; and more.")
     (inputs
      `(("python2-numpy" ,python2-numpy)))))
 
+(define-public bpp-core
+  ;; The last release was in 2014 and the recommended way to install from source
+  ;; is to clone the git repository, so we do this.
+  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
+  (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
+    (package
+      (name "bpp-core")
+      (version (string-append "2.2.0-1." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "http://biopp.univ-montp2.fr/git/bpp-core")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:parallel-build? #f))
+      (inputs
+       `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
+                          ; compile all of the bpp packages with GCC 5.
+      (home-page "http://biopp.univ-montp2.fr")
+      (synopsis "C++ libraries for Bioinformatics")
+      (description
+       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.  It is
+Object Oriented and is designed to be both easy to use and computer efficient.
+Bio++ intends to help programmers to write computer expensive programs, by
+providing them a set of re-usable tools.")
+      (license license:cecill-c))))
+
 (define-public blast+
   (package
     (name "blast+")
-- 
2.9.1

[PATCH 15/22] gnu: Add bpp-seq.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4fb23a4..4ca890c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -503,6 +503,40 @@ Bio++ intends to help programmers to write computer expensive programs, by
 providing them a set of re-usable tools.")
       (license license:cecill-c))))
 
+(define-public bpp-seq
+  ;; The last release was in 2014 and the recommended way to install from source
+  ;; is to clone the git repository, so we do this.
+  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
+  (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
+    (package
+      (name "bpp-seq")
+      (version (string-append "2.2.0-1." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "http://biopp.univ-montp2.fr/git/bpp-seq")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:parallel-build? #f
+         ;; If out-of-source, test data is not copied into the build directory
+         ;; so the tests fail.
+         #:out-of-source? #f))
+      (inputs
+       `(("bpp-core" ,bpp-core)
+         ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
+      (home-page "http://biopp.univ-montp2.fr")
+      (synopsis "Bio++ sequence library")
+      (description
+       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.  This
+library provides sequence-related modules.")
+      (license license:cecill-c))))
+
 (define-public blast+
   (package
     (name "blast+")
-- 
2.9.1

[PATCH 16/22] gnu: Add bpp-phyl.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4ca890c..803dae9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -503,6 +503,43 @@ Bio++ intends to help programmers to write computer expensive programs, by
 providing them a set of re-usable tools.")
       (license license:cecill-c))))
 
+(define-public bpp-phyl
+  ;; The last release was in 2014 and the recommended way to install from source
+  ;; is to clone the git repository, so we do this.
+  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
+  (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
+    (package
+      (name "bpp-phyl")
+      (version (string-append "2.2.0-1." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:parallel-build? #f
+         ;; If out-of-source, test data is not copied into the build directory
+         ;; so the tests fail.
+         #:out-of-source? #f))
+      (inputs
+       `(("bpp-core" ,bpp-core)
+         ("bpp-seq" ,bpp-seq)
+         ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
+         ;; modern GCC.
+         ("gcc" ,gcc-5)))
+      (home-page "http://biopp.univ-montp2.fr")
+      (synopsis "Bio++ phylogenetic Library")
+      (description
+       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.  This
+library provides phylogenetics-related modules.")
+      (license license:cecill-c))))
+
 (define-public bpp-seq
   ;; The last release was in 2014 and the recommended way to install from source
   ;; is to clone the git repository, so we do this.
-- 
2.9.1

[PATCH 17/22] gnu: Add bpp-popgen.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 803dae9..5dfc637 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -540,6 +540,39 @@ analysis, phylogenetics, molecular evolution and population genetics.  This
 library provides phylogenetics-related modules.")
       (license license:cecill-c))))
 
+(define-public bpp-popgen
+  ;; The last release was in 2014 and the recommended way to install from source
+  ;; is to clone the git repository, so we do this.
+  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
+  (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
+    (package
+      (name "bpp-popgen")
+      (version (string-append "2.2.0-1." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:parallel-build? #f
+         #:tests? #f)) ; There are no tests.
+      (inputs
+       `(("bpp-core" ,bpp-core)
+         ("bpp-seq" ,bpp-seq)
+         ("gcc" ,gcc-5)))
+      (home-page "http://biopp.univ-montp2.fr")
+      (synopsis "Bio++ population genetics library")
+      (description
+       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.  This
+library provides population genetics-related modules.")
+      (license license:cecill-c))))
+
 (define-public bpp-seq
   ;; The last release was in 2014 and the recommended way to install from source
   ;; is to clone the git repository, so we do this.
-- 
2.9.1

[PATCH 18/22] gnu: Add bppsuite.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (bppsuite): New variable.
---
 gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dfc637..5ea2240 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -51,11 +51,13 @@
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
+  #:use-module (gnu packages groff)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ncurses)
@@ -70,6 +72,7 @@
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages texinfo)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
@@ -607,6 +610,45 @@ analysis, phylogenetics, molecular evolution and population genetics.  This
 library provides sequence-related modules.")
       (license license:cecill-c))))
 
+(define-public bppsuite
+  ;; The last release was in 2014 and the recommended way to install from source
+  ;; is to clone the git repository, so we do this.
+  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
+  (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
+    (package
+      (name "bppsuite")
+      (version (string-append "2.2.0-1." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "http://biopp.univ-montp2.fr/git/bppsuite")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:parallel-build? #f
+         #:tests? #f)) ; There are no tests.
+      (native-inputs
+       `(("groff" ,groff)
+         ("man-db" ,man-db)
+         ("texinfo" ,texinfo)))
+      (inputs
+       `(("bpp-core" ,bpp-core)
+         ("bpp-seq" ,bpp-seq)
+         ("bpp-phyl" ,bpp-phyl)
+         ("bpp-phyl" ,bpp-popgen)
+         ("gcc" ,gcc-5)))
+      (home-page "http://biopp.univ-montp2.fr")
+      (synopsis "Bioinformatics tools written with the Bio++ libraries")
+      (description
+       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.  This
+package provides command line tools using the Bio++ library.")
+      (license license:cecill-c))))
+
 (define-public blast+
   (package
     (name "blast+")
-- 
2.9.1

[PATCH 19/22] gnu: Add exonerate.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (exonerate): New variable.
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5ea2240..14ac57f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -51,6 +51,7 @@
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
+  #:use-module (gnu packages glib)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
@@ -1917,6 +1918,34 @@ in structured XML format.  This can eliminate the need for writing custom
 software to answer ad hoc questions.")
     (license license:public-domain)))
 
+(define-public exonerate
+  (package
+    (name "exonerate")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
+         "exonerate-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1zz5dxhpkrv5k892kcjp3wqsw5ml54qg88lmi2gk5yl82c5p58hf"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page
+     "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
+    (synopsis "Generic tool for biological sequence alignment")
+    (description
+     "Exonerate is a generic tool for pairwise sequence comparison.  It allows
+the alignment of sequences using a many alignment models, either exhaustive
+dynamic programming or a variety of heuristics.")
+    (license license:gpl3)))
+
 (define-public express
   (package
     (name "express")
-- 
2.9.1

Re: [PATCH 19/22] gnu: Add exonerate.

[Leo Famulari]

On Wed, Jul 27, 2016 at 10:54:20PM +1000, Ben Woodcroft wrote:
> * gnu/packages/bioinformatics.scm (exonerate): New variable.

> +    (version "2.2.0")

I see versions 2.3.0 and 2.4.0 are available. Why package the older version?

[PATCH 20/22] gnu: Add prank.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (prank): New variable.
---
 gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 14ac57f..ea37a93 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3176,6 +3176,58 @@ the phenotype as it models the data.")
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public prank
+  (package
+    (name "prank")
+    (version "150803")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://wasabiapp.org/download/prank/prank.source."
+                    version ".tgz"))
+              (sha256
+               (base32
+                "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-src-dir
+            (lambda _
+              (chdir "src")
+              #t))
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1"))
+                    (path (string-append
+                           (assoc-ref %build-inputs "mafft") "/bin:"
+                           (assoc-ref %build-inputs "exonerate") "/bin:"
+                           (assoc-ref %build-inputs "bppsuite") "/bin")))
+               (install-file "prank" bin)
+               (wrap-program (string-append bin "/prank")
+                 `("PATH" ":" prefix (,path)))
+               (install-file "prank.1" man))
+             #t)))))
+    (inputs
+     `(("mafft" ,mafft)
+       ("exonerate" ,exonerate)
+       ("bppsuite" ,bppsuite)))
+    (home-page "http://wasabiapp.org/software/prank/")
+    (synopsis "Probabilistic multiple sequence alignment program")
+    (description
+     "PRANK is a probabilistic multiple sequence alignment program for DNA,
+codon and amino-acid sequences.  It is based on a novel algorithm that treats
+insertions correctly and avoids over-estimation of the number of deletion
+events.  In addition, PRANK borrows ideas from maximum likelihood methods used
+in phylogenetics and correctly takes into account the evolutionary distances
+between sequences.  Lastly, PRANK allows for defining a potential structure
+for sequences to be aligned and then, simultaneously with the alignment,
+predicts the locations of structural units in the sequences.")
+    (license license:gpl2+)))
+
 (define-public pyicoteo
   (package
     (name "pyicoteo")
-- 
2.9.1

[PATCH 21/22] gnu: Add raxml.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (raxml): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ea37a93..4e599a7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3297,6 +3297,46 @@ format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
 partial genes, and identifies translation initiation sites.")
     (license license:gpl3+)))
 
+(define-public raxml
+  (package
+    (name "raxml")
+    (version "8.2.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "https://github.com/stamatak/standard-RAxML/archive/v"
+         version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; There are no tests.
+       ;; Use 'standard' Makefile rather than SSE or AVX ones.
+       #:make-flags (list "-f" "Makefile.HYBRID.gcc")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (executable "raxmlHPC-HYBRID"))
+               (install-file executable bin)
+               (symlink (string-append bin "/" executable) "raxml"))
+             #t)))))
+    (inputs
+     `(("openmpi" ,openmpi)))
+    (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
+    (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
+    (description
+     "RAxML is a tool for phylogenetic analysis and post-analysis of large
+phylogenies.")
+    (license license:gpl2+)))
+
 (define-public rsem
   (package
     (name "rsem")
-- 
2.9.1

[PATCH 22/22] gnu: Add roary.

[Ben Woodcroft]

* gnu/packages/bioinformatics.scm (roary): New variable.
---
 gnu/packages/bioinformatics.scm | 120 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 120 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4e599a7..7d4139b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -63,6 +63,7 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pcre)
+  #:use-module (gnu packages parallel)
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
@@ -3297,6 +3298,125 @@ format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
 partial genes, and identifies translation initiation sites.")
     (license license:gpl3+)))
 
+(define-public roary
+  (package
+    (name "roary")
+    (version "3.6.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1qscm97xa6vxxxlbh730gyp3b001abcg8iy2hvaqymc596x7hpi3"))))
+    (build-system perl-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-bundled-binaries
+           (lambda _
+             (delete-file-recursively "binaries")
+             #t))
+         (delete 'configure)
+         (delete 'build)
+         (replace 'check
+           (lambda _
+             ;; The tests are not run by default, so we run each test file
+             ;; directly.
+             (setenv "PATH" (string-append (getcwd) "/bin" ":"
+                                           (getenv "PATH")))
+             (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
+                                               (getenv "PERL5LIB")))
+             (zero? (length (filter (lambda (file)
+                                      (display file)(display "\n")
+                                      (not (zero? (system* "perl" file))))
+                                    (find-files "t" ".*\\.t$"))))))
+         (replace 'install
+           ;; There is no 'install' target in the Makefile.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (perl (string-append out "/lib/perl5/site_perl"))
+                    (roary-plots "contrib/roary_plots"))
+               (mkdir-p bin)
+               (mkdir-p perl)
+               (copy-recursively "bin" bin)
+               (copy-recursively "lib" perl)
+               #t)))
+         (add-after 'install 'wrap-programs
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (perl5lib (getenv "PERL5LIB"))
+                    (path (getenv "PATH")))
+               (for-each (lambda (prog)
+                           (let ((binary (string-append out "/" prog)))
+                             (wrap-program binary
+                               `("PERL5LIB" ":" prefix
+                                 (,(string-append perl5lib ":" out
+                                                  "/lib/perl5/site_perl"))))
+                             (wrap-program binary
+                               `("PATH" ":" prefix
+                                 (,(string-append path ":" out "/bin"))))))
+                         (find-files "bin" ".*[^R]$"))
+               (let ((file
+                      (string-append out "/bin/roary-create_pan_genome_plots.R"))
+                     (r-site-lib (getenv "R_LIBS_SITE"))
+                     (coreutils-path
+                      (string-append (assoc-ref inputs "coreutils") "/bin")))
+                 (wrap-program file
+                   `("R_LIBS_SITE" ":" prefix
+                     (,(string-append r-site-lib ":" out "/site-library/"))))
+                 (wrap-program file
+                   `("PATH" ":" prefix
+                     (,(string-append coreutils-path ":" out "/bin"))))))
+             #t)))))
+    (native-inputs
+     `(("perl-env-path" ,perl-env-path)
+       ("perl-test-files" ,perl-test-files)
+       ("perl-test-most" ,perl-test-most)
+       ("perl-test-output" ,perl-test-output)))
+    (inputs
+     `(("perl-array-utils" ,perl-array-utils)
+       ("bioperl" ,bioperl-minimal)
+       ("perl-exception-class" ,perl-exception-class)
+       ("perl-file-find-rule" ,perl-file-find-rule)
+       ("perl-file-grep" ,perl-file-grep)
+       ("perl-file-slurper" ,perl-file-slurper)
+       ("perl-file-which" ,perl-file-which)
+       ("perl-graph" ,perl-graph)
+       ("perl-graph-readwrite" ,perl-graph-readwrite)
+       ("perl-log-log4perl" ,perl-log-log4perl)
+       ("perl-moose" ,perl-moose)
+       ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
+       ("perl-text-csv" ,perl-text-csv)
+       ("bedtools" ,bedtools)
+       ("cd-hit" ,cd-hit)
+       ("blast+" ,blast+)
+       ("mcl" ,mcl)
+       ("parallel" ,parallel)
+       ("prank" ,prank)
+       ("mafft" ,mafft)
+       ("fasttree" ,fasttree)
+       ("grep" ,grep)
+       ("sed" ,sed)
+       ("gawk" ,gawk)
+       ("r" ,r)
+       ("r-ggplot2" ,r-ggplot2)
+       ("coreutils" ,coreutils)))
+    (home-page "http://sanger-pathogens.github.io/Roary")
+    (synopsis "High speed stand-alone pan genome pipeline")
+    (description
+     "Roary is a high speed stand alone pan genome pipeline, which takes
+annotated assemblies in GFF3 format (produced by the Prokka program) and
+calculates the pan genome.  Using a standard desktop PC, it can analyse
+datasets with thousands of samples, without compromising the quality of the
+results.  128 samples can be analysed in under 1 hour using 1 GB of RAM and a
+single processor.  Roary is not intended for meta-genomics or for comparing
+extremely diverse sets of genomes.")
+    (license license:gpl3)))
+
 (define-public raxml
   (package
     (name "raxml")
-- 
2.9.1

Re: [PATCH 22/22] gnu: Add roary.

[Leo Famulari]

On Wed, Jul 27, 2016 at 10:54:23PM +1000, Ben Woodcroft wrote:
> * gnu/packages/bioinformatics.scm (roary): New variable.

Wow, this is a complicated package! Thanks for doing the work!

> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'delete-bundled-binaries
> +           (lambda _
> +             (delete-file-recursively "binaries")
> +             #t))

The only thing I would suggest you change is to delete these binaries in
an origin snippet. The effect would be that the binaries would not be
provided by `guix build --source roary`.

If the binaries aren't provided with their source code, then I think
this change is required.

Re: [PATCH 01/22] gnu: parallel: Use full paths for executables.

[Leo Famulari]

On Wed, Jul 27, 2016 at 10:54:02PM +1000, Ben Woodcroft wrote:
> * gnu/packages/parallel.scm (parallel)[inputs]: Add procps.
> [arguments]: New field.

> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'patch-bin-sh
> +           (lambda _
> +             (for-each
> +              (lambda (file)
> +                (substitute* file
> +                  ;; Patch hard coded '/bin/sh' in the lin ending in:
> +                  ;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
> +                  ;;  parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
> +                  (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))
> +                  ;; Patch call to 'ps' and 'perl' commands.
> +                  ((" ps ") (string-append " " (which "ps") " "))
> +                  ((" perl -") (string-append " " (which "perl") " -"))))
> +              (list "src/parallel" "src/sem"))))
> +         (add-after 'install 'post-install-test
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (zero? (system* (string-append
> +                              (assoc-ref outputs "out") "/bin/parallel")
> +                             "echo"
> +                             ":::" "1" "2" "3")))))))

Do we need the 'post-install-test' phase, or was it left in by accident after
debugging?

Re: PATCH [0/22]: Add roary.

[Ludovic Courtès]

Hello,

Ben Woodcroft <donttrustben@gmail.com> skribis:

> This patchset adds roary, a pipeline which at times is used for tracking
> outbreaks of pathogenic bacteria in e.g. foodstuffs or hospitals, by comparing
> whole genome sequences.

I looked briefly at this series and I guess you can take into account
Leo’s comments and the push.

> perl-log-log4perl was already discussed previously and I am happy to
> defer to that patch.  I only include mine here so the packages build.
> https://lists.gnu.org/archive/html/guix-devel/2016-07/msg00624.html

Alex, have you pushed it yet?

Thank you Ben for this heroic packaging effort!  :-)

Ludo’.

Re: PATCH [0/22]: Add roary.

[Ben Woodcroft]

Hi,


On 31/07/16 21:26, Ludovic Courtès wrote:
> Hello,
>
> Ben Woodcroft <donttrustben@gmail.com> skribis:
>
>> This patchset adds roary, a pipeline which at times is used for tracking
>> outbreaks of pathogenic bacteria in e.g. foodstuffs or hospitals, by comparing
>> whole genome sequences.
> I looked briefly at this series and I guess you can take into account
> Leo’s comments and the push.

Thanks, all your comments were helpful Leo. I pushed these after minor 
modifications now that Alex pushed his log4perl patch.
ben