Hi,
I've been a little while responding as I intending on releasing a new
OrfM version before bothering you again. I'd push all this myself but
wanted to check one last thing so I don't sound too enthusiastic about
my own software.
+
+(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.")
I don’t really like the first sentence. How about
“Bio-comandeer lets you run shell commands from within Ruby. ...”
That wasn't the best sentence before, fo so. I wonder if the replacement
is a little bland though. How about (as attached),
+ "Bio-commandeer provides an 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
@code{STDOUT}
+and @code{STDERR} are reported, giving extra detail to ease debugging.")
OK? I made scattered other changes too on top of accepting your
suggestions, but I don't imagine a full re-review is necessary.
Thanks for the review.
ben
>From 5d535f5c465c947140a2917fb9c0aaa31b651102 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 0.5.3.
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
---
gnu/packages/bioinformatics.scm | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82506c1..9c2223f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2079,7 +2079,7 @@ that a read originated from a particular isoform.")
(define-public orfm
(package
(name "orfm")
- (version "0.4.1")
+ (version "0.5.3")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2087,12 +2087,16 @@ that a read originated from a particular isoform.")
version "/orfm-" version ".tar.gz"))
(sha256
(base32
- "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"))))
+ "0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk"))))
(build-system gnu-build-system)
(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
+ "An ORF caller finds stretches of DNA that, when translated, are not
interrupted by stop codons. OrfM finds and prints these ORFs.")
(home-page "https://github.com/wwood/OrfM";)
(license license:lgpl3+)))
--
2.6.3
>From 4ded5e53c22ada399c976989dbe10cbf376c4e98 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 | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 21f282a..59fe1cd 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2958,3 +2958,38 @@ 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 provides an 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 @code{STDOUT}
+and @code{STDERR} are reported, giving extra detail to ease debugging.")
+ (home-page "http://github.com/wwood/bioruby-commandeer";)
+ (license license:expat)))
--
2.6.3
>From b7d92cbfd47fa9f4807ea72d570d703b78fb59f7 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 | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 577be18..21f282a 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2930,3 +2930,31 @@ methods, a @code{Mixin} module for including color methods, a @code{Logger}, a
device.")
(home-page "http://rubyworks.github.io/ansi";)
(license license:bsd-2)))
+
+(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-and-set-version
+ (lambda _
+ (setenv "VERSION" ,version)
+ #t)))))
+ (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 @code{open3} and @code{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)))
--
2.6.3
