Perhaps this set could be seen as a little self-serving given I'm the
author, though at least ruby-systemu is more widely used.
Thanks in advance for review.
ben
>From 6aad034b3d40bffe2bec35ed3f7df7ce1537217d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 21 Nov 2015 10:02:11 +1000
Subject: [PATCH 1/3] gnu: Add ruby-systemu.
* gnu/packages/ruby.scm (ruby-systemu): New variable.
---
gnu/packages/ruby.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 7c12421..ad20b73 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2060,3 +2060,33 @@ programs to concentrate on the implementation of network protocols. It can be
used to create both network servers and clients.")
(home-page "http://rubyeventmachine.com")
(license (list license:ruby license:gpl3)))) ; GPLv3 only AFAICT
+
+(define-public ruby-systemu
+ (package
+ (name "ruby-systemu")
+ (version "2.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "systemu" version))
+ (sha256
+ (base32
+ "0gmkbakhfci5wnmbfx5i54f25j9zsvbw858yg3jjhfs5n4ad1xq1"))))
+ (build-system ruby-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'patch-version
+ (lambda _
+ (substitute* "Rakefile"
+ ((" This.lib = lib")
+ " This.lib = 'systemu'")
+ ((" version = ENV\\['VERSION'\\]")
+ (string-append "version='" ,version "'"))))))))
+ (synopsis "Capture of stdout/stderr and handling of child processes")
+ (description
+ "Systemu can be used on any platform to return status, stdout, and stderr
+of any command. Unlike other methods like open3/popen4 there is no danger of
+full pipes or threading issues hanging your process or subprocess.")
+ (home-page "https://github.com/ahoward/systemu")
+ (license license:ruby)))
--
2.1.4
>From b1981255c06271c8cd4f3fd5291414034714cd2f Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 21 Nov 2015 10:03:41 +1000
Subject: [PATCH 2/3] gnu: Add ruby-bio-commandeer.
* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
---
gnu/packages/ruby.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index ad20b73..c964fe3 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2090,3 +2090,39 @@ of any command. Unlike other methods like open3/popen4 there is no danger of
full pipes or threading issues hanging your process or subprocess.")
(home-page "https://github.com/ahoward/systemu")
(license license:ruby)))
+
+(define-public ruby-bio-commandeer
+ (package
+ (name "ruby-bio-commandeer")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-commandeer" version))
+ (sha256
+ (base32
+ "061jxa6km92qfwzl058r2gp8gfcsbyr7m643nw1pxvmjdswaf6ly"))))
+ (build-system ruby-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ ;; Run test without calling 'rake' so that jeweler is
+ ;; not required as an input.
+ (lambda _
+ (zero? (system* "rspec" "spec/bio-commandeer_spec.rb")))))))
+ (propagated-inputs
+ `(("ruby-bio-logger" ,ruby-bio-logger)
+ ("ruby-systemu" ,ruby-systemu)))
+ (native-inputs
+ `(("bundler" ,bundler)
+ ("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Simplified running of shell commands from within Ruby")
+ (description
+ "Bio-commandeer is a dead simple opinionated method of running shell
+commands from within Ruby. The advantage of bio-commandeer over other methods
+of running external commands is that when something goes wrong, the error
+message that is reported gives extra detail to ease debugging.")
+ (home-page
+ "http://github.com/wwood/bioruby-commandeer")
+ (license license:expat)))
--
2.1.4
>From 1fe31024e6c78ab7bbdfe7be2c2ac8f4ec1db447 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 21 Nov 2015 10:37:34 +1000
Subject: [PATCH 3/3] gnu: orfm: Update to 0.4.4.
* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.4.
[arguments]: Run intended tests.
[inputs]: Add inputs required for tests.
---
gnu/packages/bioinformatics.scm | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35cec1e..24a1992 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1878,7 +1878,7 @@ that a read originated from a particular isoform.")
(define-public orfm
(package
(name "orfm")
- (version "0.4.1")
+ (version "0.4.4")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1886,9 +1886,15 @@ that a read originated from a particular isoform.")
version "/orfm-" version ".tar.gz"))
(sha256
(base32
- "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"))))
+ "1pwpy6qwkjjd4jyfln5c4c0009blgar0g7c5wkldbs9mzqrv77di"))))
(build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"))
(inputs `(("zlib" ,zlib)))
+ (native-inputs
+ `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
+ ("ruby-rspec" ,ruby-rspec)
+ ("ruby" ,ruby)))
(synopsis "Simple and not slow open reading frame (ORF) caller")
(description
"An ORF caller finds stretches of DNA that when translated are not
--
2.1.4