* [PATCH] Add SortMeRNA.
@ 2016-01-22 12:12 Ben Woodcroft
2016-01-22 20:35 ` Leo Famulari
0 siblings, 1 reply; 5+ messages in thread
From: Ben Woodcroft @ 2016-01-22 12:12 UTC (permalink / raw)
To: guix-devel@gnu.org
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Thanks in advance as usual.
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From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 16 Jan 2016 13:33:08 +1000
Subject: [PATCH] gnu: Add sortmerna.
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e579afe..e170ff7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3016,6 +3016,45 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
of these reads to align data quickly through a hash-based indexing scheme.")
(license license:asl2.0)))
+(define-public sortmerna
+ (package
+ (name "sortmerna")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/biocore/sortmerna/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (share (string-append out "/share/sortmerna/rRNA_databases")))
+ (install-file "sortmerna" bin)
+ (install-file "indexdb_rna" bin)
+ (for-each (lambda (file)
+ (install-file file share))
+ (find-files "rRNA_databases" ".*fasta"))
+ #t))))))
+ (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
+ (synopsis "Biological sequence analysis tool for NGS reads")
+ (description
+ "SortMeRNA is a biological sequence analysis tool for filtering, mapping
+and operational taxonomic unit (OTU) picking next generation sequencing reads.
+The core algorithm is based on approximate seeds and allows for fast and
+sensitive analyses of nucleotide sequences. The main application of SortMeRNA
+is filtering rRNA from metatranscriptomic data.")
+ (license license:lgpl3)))
+
(define-public star
(package
(name "star")
--
2.6.3
^ permalink raw reply related [flat|nested] 5+ messages in thread* Re: [PATCH] Add SortMeRNA.
2016-01-22 12:12 [PATCH] Add SortMeRNA Ben Woodcroft
@ 2016-01-22 20:35 ` Leo Famulari
2016-01-22 21:55 ` Ben Woodcroft
0 siblings, 1 reply; 5+ messages in thread
From: Leo Famulari @ 2016-01-22 20:35 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> Thanks in advance as usual.
> From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Sat, 16 Jan 2016 13:33:08 +1000
> Subject: [PATCH] gnu: Add sortmerna.
>
> * gnu/packages/bioinformatics.scm (sortmerna): New variable.
> ---
> gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
> 1 file changed, 39 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index e579afe..e170ff7 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -3016,6 +3016,45 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
> of these reads to align data quickly through a hash-based indexing scheme.")
> (license license:asl2.0)))
>
> +(define-public sortmerna
> + (package
> + (name "sortmerna")
> + (version "2.0")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (string-append
> + "https://github.com/biocore/sortmerna/archive/"
> + version ".tar.gz"))
> + (file-name (string-append name "-" version ".tar.gz"))
> + (sha256
> + (base32
> + "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
> + (build-system gnu-build-system)
> + (arguments
> + `(#:phases
> + (modify-phases %standard-phases
My sense of Scheme style is still pretty weak but shouldn't the above
line move one character to the right (along with the remainder of
arguments)?
> + (replace 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let* ((out (assoc-ref outputs "out"))
> + (bin (string-append out "/bin"))
> + (share (string-append out "/share/sortmerna/rRNA_databases")))
> + (install-file "sortmerna" bin)
> + (install-file "indexdb_rna" bin)
> + (for-each (lambda (file)
> + (install-file file share))
> + (find-files "rRNA_databases" ".*fasta"))
> + #t))))))
> + (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
> + (synopsis "Biological sequence analysis tool for NGS reads")
Does it make sense to explain the "NGS" acronym anywhere?
> + (description
> + "SortMeRNA is a biological sequence analysis tool for filtering, mapping
> +and operational taxonomic unit (OTU) picking next generation sequencing reads.
Does this sentence make more sense with "of" inserted between "picking"
and "next"?
> +The core algorithm is based on approximate seeds and allows for fast and
> +sensitive analyses of nucleotide sequences. The main application of SortMeRNA
> +is filtering rRNA from metatranscriptomic data.")
> + (license license:lgpl3)))
> +
> (define-public star
> (package
> (name "star")
> --
> 2.6.3
>
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Add SortMeRNA.
2016-01-22 20:35 ` Leo Famulari
@ 2016-01-22 21:55 ` Ben Woodcroft
2016-01-22 23:00 ` Leo Famulari
0 siblings, 1 reply; 5+ messages in thread
From: Ben Woodcroft @ 2016-01-22 21:55 UTC (permalink / raw)
To: Leo Famulari; +Cc: guix-devel@gnu.org
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On 23/01/16 06:35, Leo Famulari wrote:
> On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
[..]
Thanks Leo. As well as responding to your review the attached patch
breaks out the rRNA databases out into a separate output "db", removing
73MB from the default package. Is "db" a good name?
> On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
[..]
>> +(define-public sortmerna
>> + (package
>> + (name "sortmerna")
>> + (version "2.0")
>> + (source
>> + (origin
>> + (method url-fetch)
>> + (uri (string-append
>> + "https://github.com/biocore/sortmerna/archive/"
>> + version ".tar.gz"))
>> + (file-name (string-append name "-" version ".tar.gz"))
>> + (sha256
>> + (base32
>> + "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
>> + (build-system gnu-build-system)
>> + (arguments
>> + `(#:phases
>> + (modify-phases %standard-phases
> > My sense of Scheme style is still pretty weak but shouldn't the >
above line move one character to the right (along with the remainder >
of arguments)?
I don't think so. I'm just trusting the tab key and other packages
around. No?
>> + (replace 'install + (lambda* (#:key outputs >> #:allow-other-keys) + (let* ((out (assoc-ref outputs
>> "out")) + (bin (string-append out "/bin")) + >>
(share (string-append out "/share/sortmerna/rRNA_databases"))) + >>
(install-file "sortmerna" bin) + (install-file >>
"indexdb_rna" bin) + (for-each (lambda (file) + >>
(install-file file share)) + (find-files >>
"rRNA_databases" ".*fasta")) + #t)))))) + >> (home-page
"http://bioinfo.lifl.fr/RNA/sortmerna") + (synopsis >> "Biological
sequence analysis tool for NGS reads") > > Does it make sense to explain
the "NGS" acronym anywhere?
OK, I've explained it in the description.
>> + (description + "SortMeRNA is a biological sequence >> analysis tool for filtering, mapping +and operational taxonomic >>
unit (OTU) picking next generation sequencing reads. > > Does this
sentence make more sense with "of" inserted between > "picking" and "next"?
I think either way is fine, but including the of rolls of the tongue a
bit better.
ben
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From 6f2599eff86b5a67a92429756f2df3ba2cf53201 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 16 Jan 2016 13:33:08 +1000
Subject: [PATCH] gnu: Add sortmerna.
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e579afe..946083f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3016,6 +3016,49 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
of these reads to align data quickly through a hash-based indexing scheme.")
(license license:asl2.0)))
+(define-public sortmerna
+ (package
+ (name "sortmerna")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/biocore/sortmerna/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
+ (build-system gnu-build-system)
+ (outputs '("out" ;for binaries
+ "db")) ;for sequence databases
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (db (assoc-ref outputs "db"))
+ (share
+ (string-append db "/share/sortmerna/rRNA_databases")))
+ (install-file "sortmerna" bin)
+ (install-file "indexdb_rna" bin)
+ (for-each (lambda (file)
+ (install-file file share))
+ (find-files "rRNA_databases" ".*fasta"))
+ #t))))))
+ (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
+ (synopsis "Biological sequence analysis tool for NGS reads")
+ (description
+ "SortMeRNA is a biological sequence analysis tool for filtering, mapping
+and operational taxonomic unit (OTU) picking of next generation
+sequencing (NGS) reads. The core algorithm is based on approximate seeds and
+allows for fast and sensitive analyses of nucleotide sequences. The main
+application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
+ (license license:lgpl3)))
+
(define-public star
(package
(name "star")
--
2.6.3
^ permalink raw reply related [flat|nested] 5+ messages in thread* Re: [PATCH] Add SortMeRNA.
2016-01-22 21:55 ` Ben Woodcroft
@ 2016-01-22 23:00 ` Leo Famulari
2016-01-24 22:36 ` Ben Woodcroft
0 siblings, 1 reply; 5+ messages in thread
From: Leo Famulari @ 2016-01-22 23:00 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
On Sat, Jan 23, 2016 at 07:55:37AM +1000, Ben Woodcroft wrote:
>
> On 23/01/16 06:35, Leo Famulari wrote:
> >On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> [..]
>
> Thanks Leo. As well as responding to your review the attached patch breaks
> out the rRNA databases out into a separate output "db", removing 73MB from
> the default package. Is "db" a good name?
Sounds like a good name. It's a good idea to split the package up if the
database is not necessary for a basic installation. I haven't used
multiple outputs in my packages yet so I can't say if your
implementation is correct or not.
> >On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> [..]
> >>+ (arguments
> >>+ `(#:phases
> >>+ (modify-phases %standard-phases
> >> My sense of Scheme style is still pretty weak but shouldn't the >
> above line move one character to the right (along with the remainder > of
> arguments)?
> I don't think so. I'm just trusting the tab key and other packages around.
> No?
Like I said, my sense of style is not very developed ;) I checked some
other packages and they agree with you.
> >>+ (description + "SortMeRNA is a biological sequence >> analysis
> >>tool for filtering, mapping +and operational taxonomic >>
> unit (OTU) picking next generation sequencing reads. > > Does this sentence
> make more sense with "of" inserted between > "picking" and "next"?
> I think either way is fine, but including the of rolls of the tongue a bit
> better.
The original was a garden path sentence to my ears. However, I am
reading the sentence as a layperson so the meaning is mostly lost on me.
>
>
> ben
>
> From 6f2599eff86b5a67a92429756f2df3ba2cf53201 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Sat, 16 Jan 2016 13:33:08 +1000
> Subject: [PATCH] gnu: Add sortmerna.
>
> * gnu/packages/bioinformatics.scm (sortmerna): New variable.
> ---
> gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 43 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index e579afe..946083f 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -3016,6 +3016,49 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
> of these reads to align data quickly through a hash-based indexing scheme.")
> (license license:asl2.0)))
>
> +(define-public sortmerna
> + (package
> + (name "sortmerna")
> + (version "2.0")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (string-append
> + "https://github.com/biocore/sortmerna/archive/"
> + version ".tar.gz"))
> + (file-name (string-append name "-" version ".tar.gz"))
> + (sha256
> + (base32
> + "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
> + (build-system gnu-build-system)
> + (outputs '("out" ;for binaries
> + "db")) ;for sequence databases
> + (arguments
> + `(#:phases
> + (modify-phases %standard-phases
> + (replace 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let* ((out (assoc-ref outputs "out"))
> + (bin (string-append out "/bin"))
> + (db (assoc-ref outputs "db"))
> + (share
> + (string-append db "/share/sortmerna/rRNA_databases")))
> + (install-file "sortmerna" bin)
> + (install-file "indexdb_rna" bin)
> + (for-each (lambda (file)
> + (install-file file share))
> + (find-files "rRNA_databases" ".*fasta"))
> + #t))))))
> + (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
> + (synopsis "Biological sequence analysis tool for NGS reads")
> + (description
> + "SortMeRNA is a biological sequence analysis tool for filtering, mapping
> +and operational taxonomic unit (OTU) picking of next generation
> +sequencing (NGS) reads. The core algorithm is based on approximate seeds and
> +allows for fast and sensitive analyses of nucleotide sequences. The main
> +application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
> + (license license:lgpl3)))
> +
> (define-public star
> (package
> (name "star")
> --
> 2.6.3
>
^ permalink raw reply [flat|nested] 5+ messages in thread* Re: [PATCH] Add SortMeRNA.
2016-01-22 23:00 ` Leo Famulari
@ 2016-01-24 22:36 ` Ben Woodcroft
0 siblings, 0 replies; 5+ messages in thread
From: Ben Woodcroft @ 2016-01-24 22:36 UTC (permalink / raw)
To: Leo Famulari; +Cc: guix-devel@gnu.org
On 23/01/16 09:00, Leo Famulari wrote:
> On Sat, Jan 23, 2016 at 07:55:37AM +1000, Ben Woodcroft wrote:
>> On 23/01/16 06:35, Leo Famulari wrote:
>>> On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
>> [..]
>>
>> Thanks Leo. As well as responding to your review the attached patch breaks
>> out the rRNA databases out into a separate output "db", removing 73MB from
>> the default package. Is "db" a good name?
> Sounds like a good name. It's a good idea to split the package up if the
> database is not necessary for a basic installation. I haven't used
> multiple outputs in my packages yet so I can't say if your
> implementation is correct or not.
I went ahead and pushed just now. Thanks for the reviews.
ben
^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2016-01-24 22:37 UTC | newest]
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2016-01-22 12:12 [PATCH] Add SortMeRNA Ben Woodcroft
2016-01-22 20:35 ` Leo Famulari
2016-01-22 21:55 ` Ben Woodcroft
2016-01-22 23:00 ` Leo Famulari
2016-01-24 22:36 ` Ben Woodcroft
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