* [PATCH 02/22] gnu: Add perl-xml-writer.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 03/22] gnu: Add perl-parse-yapp Ben Woodcroft
` (20 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
2016-07-27 12:54 ` [PATCH 02/22] gnu: Add perl-xml-writer Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 04/22] gnu: Add perl-graph Ben Woodcroft
` (19 subsequent siblings)
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 04/22] gnu: Add perl-graph.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
2016-07-27 12:54 ` [PATCH 02/22] gnu: Add perl-xml-writer Ben Woodcroft
2016-07-27 12:54 ` [PATCH 03/22] gnu: Add perl-parse-yapp Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 05/22] gnu: Add perl-graph-readwrite Ben Woodcroft
` (18 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 05/22] gnu: Add perl-graph-readwrite.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (2 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 04/22] gnu: Add perl-graph Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 06/22] gnu: Add perl-log-log4perl Ben Woodcroft
` (17 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 06/22] gnu: Add perl-log-log4perl.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (3 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 05/22] gnu: Add perl-graph-readwrite Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 07/22] gnu: Add perl-file-slurper Ben Woodcroft
` (16 subsequent siblings)
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 07/22] gnu: Add perl-file-slurper.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (4 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 06/22] gnu: Add perl-log-log4perl Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 08/22] gnu: Add perl-file-path Ben Woodcroft
` (15 subsequent siblings)
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (5 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 07/22] gnu: Add perl-file-slurper Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 09/22] gnu: Add perl-file-grep Ben Woodcroft
` (14 subsequent siblings)
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (6 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 08/22] gnu: Add perl-file-path Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 10/22] gnu: Add perl-array-utils Ben Woodcroft
` (13 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (7 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 09/22] gnu: Add perl-file-grep Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 11/22] gnu: Add perl-test-files Ben Woodcroft
` (12 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (8 preceding siblings ...)
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@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 12/22] gnu: Add perl-env-path Ben Woodcroft
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (9 preceding siblings ...)
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@ 2016-07-27 12:54 ` Ben Woodcroft
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (10 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 12/22] gnu: Add perl-env-path Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-28 22:20 ` Leo Famulari
2016-07-27 12:54 ` [PATCH 14/22] gnu: Add bpp-core Ben Woodcroft
` (9 subsequent siblings)
21 siblings, 1 reply; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 15/22] gnu: Add bpp-seq Ben Woodcroft
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From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (12 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 14/22] gnu: Add bpp-core Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 16/22] gnu: Add bpp-phyl Ben Woodcroft
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21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (13 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 15/22] gnu: Add bpp-seq Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 17/22] gnu: Add bpp-popgen Ben Woodcroft
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21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (14 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 16/22] gnu: Add bpp-phyl Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 18/22] gnu: Add bppsuite Ben Woodcroft
` (5 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 18/22] gnu: Add bppsuite.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (15 preceding siblings ...)
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@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 19/22] gnu: Add exonerate Ben Woodcroft
` (4 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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` (16 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 18/22] gnu: Add bppsuite Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-28 22:22 ` Leo Famulari
2016-07-27 12:54 ` [PATCH 20/22] gnu: Add prank Ben Woodcroft
` (3 subsequent siblings)
21 siblings, 1 reply; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
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@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 21/22] gnu: Add raxml Ben Woodcroft
` (2 subsequent siblings)
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 21/22] gnu: Add raxml.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (18 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 20/22] gnu: Add prank Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-27 12:54 ` [PATCH 22/22] gnu: Add roary Ben Woodcroft
2016-07-28 22:31 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Leo Famulari
21 siblings, 0 replies; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [PATCH 22/22] gnu: Add roary.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (19 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 21/22] gnu: Add raxml Ben Woodcroft
@ 2016-07-27 12:54 ` Ben Woodcroft
2016-07-29 21:07 ` Leo Famulari
2016-07-28 22:31 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Leo Famulari
21 siblings, 1 reply; 29+ messages in thread
From: Ben Woodcroft @ 2016-07-27 12:54 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 29+ messages in thread* Re: [PATCH 22/22] gnu: Add roary.
2016-07-27 12:54 ` [PATCH 22/22] gnu: Add roary Ben Woodcroft
@ 2016-07-29 21:07 ` Leo Famulari
0 siblings, 0 replies; 29+ messages in thread
From: Leo Famulari @ 2016-07-29 21:07 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel
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.
^ permalink raw reply [flat|nested] 29+ messages in thread
* Re: [PATCH 01/22] gnu: parallel: Use full paths for executables.
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
` (20 preceding siblings ...)
2016-07-27 12:54 ` [PATCH 22/22] gnu: Add roary Ben Woodcroft
@ 2016-07-28 22:31 ` Leo Famulari
21 siblings, 0 replies; 29+ messages in thread
From: Leo Famulari @ 2016-07-28 22:31 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel
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?
^ permalink raw reply [flat|nested] 29+ messages in thread