[PATCH] Add prodigal.

[PATCH] Add prodigal.

[Ben Woodcroft]

[-- Attachment #1: Type: text/plain, Size: 37 bytes --]

A popular tool in microbial ecology.

[-- Attachment #2: 0001-gnu-Add-prodigal.patch --]
[-- Type: text/x-patch, Size: 2235 bytes --]

From ebec585b41d6a2bad6b9b04b07f0003ede389f1a Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 27 Jun 2015 09:24:08 +1000
Subject: [PATCH] gnu: Add prodigal.

* gnu/packages/bioinformatics.scm (prodigal): 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 31df219..8c6b010 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1405,6 +1405,40 @@ files and writing bioinformatics applications.")
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public prodigal
+  (package
+    (name "prodigal")
+    (version "2.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/hyattpd/Prodigal/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no check target
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (let ((bin (string-append (assoc-ref outputs "out")
+                                              "/bin")))
+                      (mkdir-p bin)
+                      (copy-file "prodigal" (string-append bin "/prodigal"))
+                      #t))))))
+    (home-page "http://prodigal.ornl.gov")
+    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
+    (description
+     "Prodigal runs smoothly on finished genomes, draft genomes, and
+metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
+format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
+partial genes, and identifies translation initiation sites.")
+    (license license:gpl3+)))
+
 (define-public rsem
   (package
     (name "rsem")
-- 
2.4.3

Re: [PATCH] Add prodigal.

[Ben Woodcroft]

[-- Attachment #1: Type: text/plain, Size: 114 bytes --]

Oops, now all lines <= 80 chars.

On 27/06/15 09:26, Ben Woodcroft wrote:
> A popular tool in microbial ecology.


[-- Attachment #2: 0001-gnu-Add-prodigal.patch --]
[-- Type: text/x-patch, Size: 2243 bytes --]

From 6e81c91c5e444cddf6e193f22d212b1eee3a5cab Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 27 Jun 2015 09:29:23 +1000
Subject: [PATCH] gnu: Add prodigal.

* gnu/packages/bioinformatics.scm (prodigal): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 31df219..40a7d78 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1405,6 +1405,41 @@ files and writing bioinformatics applications.")
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public prodigal
+  (package
+    (name "prodigal")
+    (version "2.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/hyattpd/Prodigal/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no check target
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (let ((bin (string-append (assoc-ref outputs "out")
+                                              "/bin")))
+                      (mkdir-p bin)
+                      (copy-file "prodigal" (string-append bin "/prodigal"))
+                      #t))))))
+    (home-page "http://prodigal.ornl.gov")
+    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
+    (description
+     "Prodigal runs smoothly on finished genomes, draft genomes, and
+metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
+format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
+partial genes, and identifies translation initiation sites.")
+    (license license:gpl3+)))
+
 (define-public rsem
   (package
     (name "rsem")
-- 
2.4.3

Re: [PATCH] Add prodigal.

[Ricardo Wurmus]

Hi Ben,

> Oops, now all lines <= 80 chars.

looks good to me, except for the synopsis:

>  +    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")

Shouldn’t “Archaea” and “Bacteria” both be lower-cased?

~~ Ricardo

Re: [PATCH] Add prodigal.

[Ricardo Wurmus]

Hi again,

another thing just occurred to me.  Instead of replacing the install
phase you might just overwrite the INSTALLDIR variable, something like
this:

    #:make-flags (list (string-append "INSTALLDIR="
                                      (assoc-ref %outputs "out")))

What do you think?

~~ Ricardo

Re: [PATCH] Add prodigal.

[Ben Woodcroft]

[-- Attachment #1: Type: text/plain, Size: 1307 bytes --]


On 27/06/15 20:40, Ricardo Wurmus wrote:
>>   +    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
> Shouldn’t “Archaea” and “Bacteria” both be lower-cased?
I don't believe so. As I understand it you can use "bacterial" and 
"archaeal" with lower case, but here we are referring to the domains as 
nouns.

I did take some small liberties here. The original sentence on the web was

 >Fast, reliable protein-coding gene prediction for prokaryotic genomes.

To me this is problematic in two ways:
1. It works on more than just genomes
2. There is some contention in the field about the use of "prokaryote", 
since this refers to a paraphyletic group - us humans are more closely 
related to Archaea than Bacteria.
http://link.springer.com/referenceworkentry/10.1007/978-3-642-30194-0_114

I figure it was just easier to sidestep the issue and put Archaea and 
Bacteria.
> another thing just occurred to me.  Instead of replacing the install
> phase you might just overwrite the INSTALLDIR variable, something like
> this:
>
>      #:make-flags (list (string-append "INSTALLDIR="
>                                        (assoc-ref %outputs "out")))
>
> What do you think?
That made it more concise, and maybe more future proof (though need 
added "/bin").

[-- Attachment #2: 0001-gnu-Add-prodigal.patch --]
[-- Type: text/x-patch, Size: 2050 bytes --]

From 086a910d53995cb209a7413c74705d2ad3b8e17e Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 27 Jun 2015 22:28:19 +1000
Subject: [PATCH] gnu: Add prodigal.

* gnu/packages/bioinformatics.scm (prodigal): New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 31df219..f321d82 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1405,6 +1405,37 @@ files and writing bioinformatics applications.")
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public prodigal
+  (package
+    (name "prodigal")
+    (version "2.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/hyattpd/Prodigal/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no check target
+       #:make-flags (list (string-append "INSTALLDIR="
+                                         (assoc-ref %outputs "out")
+                                         "/bin"))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (home-page "http://prodigal.ornl.gov")
+    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
+    (description
+     "Prodigal runs smoothly on finished genomes, draft genomes, and
+metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
+format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
+partial genes, and identifies translation initiation sites.")
+    (license license:gpl3+)))
+
 (define-public rsem
   (package
     (name "rsem")
-- 
2.4.3

Re: [PATCH] Add prodigal.

[Ben Woodcroft]

On 27/06/15 22:33, Ben Woodcroft wrote:
> To me this is problematic in two ways:
> 1. It works on more than just genomes
> 2. There is some contention in the field about the use of 
> "prokaryote", since this refers to a paraphyletic group - us humans 
> are more closely related to Archaea than Bacteria.
> http://link.springer.com/referenceworkentry/10.1007/978-3-642-30194-0_114
>
> I figure it was just easier to sidestep the issue and put Archaea and 
> Bacteria.
Perhaps I bored everyone, but is the patch a-ok now?

ta

Re: [PATCH] Add prodigal.

[Mark H Weaver]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> On 27/06/15 22:33, Ben Woodcroft wrote:
>> To me this is problematic in two ways:
>> 1. It works on more than just genomes
>> 2. There is some contention in the field about the use of
>> "prokaryote", since this refers to a paraphyletic group - us humans
>> are more closely related to Archaea than Bacteria.
>> http://link.springer.com/referenceworkentry/10.1007/978-3-642-30194-0_114
>>
>> I figure it was just easier to sidestep the issue and put Archaea
>> and Bacteria.
> Perhaps I bored everyone, but is the patch a-ok now?

Looks good to me.  Pushed, thanks!

     Mark

Re: [PATCH] Add prodigal.

[Alex Kost]

Ben Woodcroft (2015-07-05 07:52 +0300) wrote:

> On 27/06/15 22:33, Ben Woodcroft wrote:
>> To me this is problematic in two ways:
>> 1. It works on more than just genomes
>> 2. There is some contention in the field about the use of
>> "prokaryote", since this refers to a paraphyletic group - us humans
>> are more closely related to Archaea than Bacteria.
>> http://link.springer.com/referenceworkentry/10.1007/978-3-642-30194-0_114
>>
>> I figure it was just easier to sidestep the issue and put Archaea and
>> Bacteria.
> Perhaps I bored everyone, but is the patch a-ok now?

I've tried it and it has been built successfully, and I think it's
absolutely OK.  I have not pushed it though as Ricardo is a Master of
bioinformatics, perhaps he'll notice something I didn't.

-- 
Alex

Re: [PATCH] Add prodigal.

[Ricardo Wurmus]

Alex Kost <alezost@gmail.com> writes:
> Ricardo is a Master of bioinformatics

Haha! :)

Mark already pushed it.  I simply forgot about this patch, my apologies!

~~ Ricardo