* [PATCH] gnu: Update STAR to 2.5.0c.
@ 2016-01-19 15:29 Ricardo Wurmus
2016-01-22 10:22 ` Ben Woodcroft
2016-01-22 17:11 ` Ludovic Courtès
0 siblings, 2 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2016-01-19 15:29 UTC (permalink / raw)
To: guix-devel
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-star-Use-modify-phases-syntax.patch --]
[-- Type: text/x-patch, Size: 1622 bytes --]
From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 19 Jan 2016 16:04:01 +0100
Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
syntax.
---
gnu/packages/bioinformatics.scm | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74cadff..d30b0c9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3259,15 +3259,15 @@ of these reads to align data quickly through a hash-based indexing scheme.")
'(#:tests? #f ;no check target
#:make-flags '("STAR")
#:phases
- (alist-cons-after
- 'unpack 'enter-source-dir (lambda _ (chdir "source"))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (install-file "STAR" bin)))
- (alist-delete
- 'configure %standard-phases)))))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-source-dir
+ (lambda _ (chdir "source") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (install-file "STAR" bin))
+ #t))
+ (delete 'configure))))
(native-inputs
`(("vim" ,vim))) ; for xxd
(inputs
--
2.1.0
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0002-gnu-star-Update-to-2.5.0c.patch --]
[-- Type: text/x-patch, Size: 3766 bytes --]
From 4efd7a8afe3fbc03f59c1061e9ab2cfcb7c88160 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 19 Jan 2016 16:26:47 +0100
Subject: [PATCH 2/2] gnu: star: Update to 2.5.0c.
* gnu/packages/bioinformatics.scm (star): Update to 2.5.0c.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++--------
1 file changed, 32 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d30b0c9..20a150f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3241,19 +3241,25 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(define-public star
(package
(name "star")
- (version "2.4.2a")
+ (version "2.5.0c")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://github.com/alexdobin/STAR/archive/STAR_"
- version ".tar.gz"))
+ (uri (string-append "https://github.com/alexdobin/STAR/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
+ "1hd662ijwns6rpsd5536sm3h69yfb6xsfkrrrlnyh745gf6d5z4q"))
(modules '((guix build utils)))
(snippet
- '(substitute* "source/Makefile"
- (("/bin/rm") "rm")))))
+ '(begin
+ (substitute* "source/Makefile"
+ (("/bin/rm") "rm"))
+ ;; Remove pre-built binaries and bundled htslib sources.
+ (delete-file-recursively "bin/MacOSX_x86_64")
+ (delete-file-recursively "bin/Linux_x86_64")
+ (delete-file-recursively "source/htslib")
+ #t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no check target
@@ -3262,6 +3268,23 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(modify-phases %standard-phases
(add-after 'unpack 'enter-source-dir
(lambda _ (chdir "source") #t))
+ (add-after 'enter-source-dir 'do-not-use-bundled-htslib
+ (lambda _
+ (substitute* "Makefile"
+ (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
+ _ prefix) prefix))
+ (substitute* '("BAMfunctions.cpp"
+ "signalFromBAM.h"
+ "bam_cat.h"
+ "bam_cat.c"
+ "STAR.cpp"
+ "bamRemoveDuplicates.cpp")
+ (("#include \"htslib/([^\"]+\\.h)\"" _ header)
+ (string-append "#include <" header ">")))
+ (substitute* "IncludeDefine.h"
+ (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
+ (string-append "<" header ">")))
+ #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
@@ -3271,7 +3294,8 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(native-inputs
`(("vim" ,vim))) ; for xxd
(inputs
- `(("zlib" ,zlib)))
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)))
(home-page "https://github.com/alexdobin/STAR")
(synopsis "Universal RNA-seq aligner")
(description
--
2.1.0
^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCH] gnu: Update STAR to 2.5.0c.
2016-01-19 15:29 [PATCH] gnu: Update STAR to 2.5.0c Ricardo Wurmus
@ 2016-01-22 10:22 ` Ben Woodcroft
2016-01-23 7:38 ` Ricardo Wurmus
2016-01-22 17:11 ` Ludovic Courtès
1 sibling, 1 reply; 5+ messages in thread
From: Ben Woodcroft @ 2016-01-22 10:22 UTC (permalink / raw)
To: Ricardo Wurmus, guix-devel
Hi Ricardo,
I notice that 2.5.1a is now released - I guess you started working on
the patch before it was so.
STARlong is in the binaries that are distributed ie
https://github.com/alexdobin/STAR/tree/master/bin/Linux_x86_64
but this is not built by us since the default make target in source/ is
just STAR. Does it make sense to build STARlong as well? I have no
experience with STAR so I do not know.
Thanks,
ben
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] gnu: Update STAR to 2.5.0c.
2016-01-19 15:29 [PATCH] gnu: Update STAR to 2.5.0c Ricardo Wurmus
2016-01-22 10:22 ` Ben Woodcroft
@ 2016-01-22 17:11 ` Ludovic Courtès
2016-01-23 7:39 ` Ricardo Wurmus
1 sibling, 1 reply; 5+ messages in thread
From: Ludovic Courtès @ 2016-01-22 17:11 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 19 Jan 2016 16:04:01 +0100
> Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax.
>
> * gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
> syntax.
[...]
> From 4efd7a8afe3fbc03f59c1061e9ab2cfcb7c88160 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 19 Jan 2016 16:26:47 +0100
> Subject: [PATCH 2/2] gnu: star: Update to 2.5.0c.
>
> * gnu/packages/bioinformatics.scm (star): Update to 2.5.0c.
> [source]: Remove bundled htslib sources and pre-built binaries.
> [arguments]: Add phase "do-not-use-bundled-htslib".
> [inputs]: Add "htslib".
Both LGTM!
Ludo’.
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] gnu: Update STAR to 2.5.0c.
2016-01-22 10:22 ` Ben Woodcroft
@ 2016-01-23 7:38 ` Ricardo Wurmus
0 siblings, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2016-01-23 7:38 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> I notice that 2.5.1a is now released - I guess you started working on
> the patch before it was so.
And now 2.5.1b has been released :) I updated the commit. Thanks for
the hint.
> STARlong is in the binaries that are distributed ie
> https://github.com/alexdobin/STAR/tree/master/bin/Linux_x86_64
>
> but this is not built by us since the default make target in source/ is
> just STAR. Does it make sense to build STARlong as well? I have no
> experience with STAR so I do not know.
I don’t know about STARlong. The users here haven’t asked for it and
it’s not part of the default build. We could add it to the package I
guess, but as I have no need for it I’m not really interested in doing
this myself.
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] gnu: Update STAR to 2.5.0c.
2016-01-22 17:11 ` Ludovic Courtès
@ 2016-01-23 7:39 ` Ricardo Wurmus
0 siblings, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2016-01-23 7:39 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
Ludovic Courtès <ludo@gnu.org> writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 19 Jan 2016 16:04:01 +0100
>> Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax.
>>
>> * gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
>> syntax.
>
> [...]
>
>> From 4efd7a8afe3fbc03f59c1061e9ab2cfcb7c88160 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 19 Jan 2016 16:26:47 +0100
>> Subject: [PATCH 2/2] gnu: star: Update to 2.5.0c.
>>
>> * gnu/packages/bioinformatics.scm (star): Update to 2.5.0c.
>> [source]: Remove bundled htslib sources and pre-built binaries.
>> [arguments]: Add phase "do-not-use-bundled-htslib".
>> [inputs]: Add "htslib".
>
> Both LGTM!
Thanks. I updated to 2.5.1b and changed the commit messages
accordingly. Will push the two commits in a moment.
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2016-01-23 7:39 UTC | newest]
Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-01-19 15:29 [PATCH] gnu: Update STAR to 2.5.0c Ricardo Wurmus
2016-01-22 10:22 ` Ben Woodcroft
2016-01-23 7:38 ` Ricardo Wurmus
2016-01-22 17:11 ` Ludovic Courtès
2016-01-23 7:39 ` Ricardo Wurmus
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.