* [PATCH] Add idr.
@ 2015-06-16 9:37 Ricardo Wurmus
2015-06-16 15:36 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2015-06-16 9:37 UTC (permalink / raw
To: guix-devel
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From 815a5e24f43f61c4beb243d98beb0659bbd74b3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 16 Jun 2015 11:33:26 +0200
Subject: [PATCH] gnu: Add idr.
* gnu/packages/bioinformatics.scm (idr): New variable.
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eb15d40..ac4c50d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1061,6 +1061,46 @@ data. It also provides the bgzip, htsfile, and tabix utilities.")
;; the rest is released under the Expat license
(license (list license:expat license:bsd-3))))
+(define-public idr
+ (package
+ (name "idr")
+ (version "2.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/nboley/idr/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'install 'wrap-program
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref %outputs "out"))
+ (path (getenv "PYTHONPATH")))
+ (wrap-program (string-append out "/bin/idr")
+ `("PYTHONPATH" ":" prefix (,path))))
+ #t)))))
+ (inputs
+ `(("python-scipy" ,python-scipy)
+ ("python-numpy" ,python-numpy)
+ ("python-matplotlib" ,python-matplotlib)))
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-setuptools" ,python-setuptools)))
+ (home-page "https://github.com/nboley/idr")
+ (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
+ (description
+ "The IDR (Irreproducible Discovery Rate) framework is a unified approach
+to measure the reproducibility of findings identified from replicate
+experiments and provide highly stable thresholds based on reproducibility.")
+ (license license:gpl3+)))
+
(define-public macs
(package
(name "macs")
--
2.1.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] Add idr.
2015-06-16 9:37 [PATCH] Add idr Ricardo Wurmus
@ 2015-06-16 15:36 ` Ludovic Courtès
2015-06-17 10:51 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Ludovic Courtès @ 2015-06-16 15:36 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 815a5e24f43f61c4beb243d98beb0659bbd74b3a Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 16 Jun 2015 11:33:26 +0200
> Subject: [PATCH] gnu: Add idr.
>
> * gnu/packages/bioinformatics.scm (idr): New variable.
[...]
> + 'install 'wrap-program
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let ((out (assoc-ref %outputs "out"))
> + (path (getenv "PYTHONPATH")))
> + (wrap-program (string-append out "/bin/idr")
> + `("PYTHONPATH" ":" prefix (,path))))
Taking $PYTHONPATH as is has the effect of keeping a reference to Cython
and to setuptools, which may not be what you want, given that they are
listed as ‘native-inputs’.
Should it instead explicitly list SciPy, NumPy, and Matplotlib?
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] Add idr.
2015-06-16 15:36 ` Ludovic Courtès
@ 2015-06-17 10:51 ` Ricardo Wurmus
2015-06-21 21:13 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2015-06-17 10:51 UTC (permalink / raw
To: Ludovic Courtès; +Cc: guix-devel
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Ludovic Courtès <ludo@gnu.org> writes:
>> + 'install 'wrap-program
>> + (lambda* (#:key outputs #:allow-other-keys)
>> + (let ((out (assoc-ref %outputs "out"))
>> + (path (getenv "PYTHONPATH")))
>> + (wrap-program (string-append out "/bin/idr")
>> + `("PYTHONPATH" ":" prefix (,path))))
>
> Taking $PYTHONPATH as is has the effect of keeping a reference to Cython
> and to setuptools, which may not be what you want, given that they are
> listed as ‘native-inputs’.
>
> Should it instead explicitly list SciPy, NumPy, and Matplotlib?
You are right. Is the attached patch better?
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From 37db5b51fe4a09496e149d59b64aa0b69ae42fd1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 16 Jun 2015 11:33:26 +0200
Subject: [PATCH] gnu: Add idr.
* gnu/packages/bioinformatics.scm (idr): New variable.
---
gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eb15d40..f243904 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1061,6 +1061,56 @@ data. It also provides the bgzip, htsfile, and tabix utilities.")
;; the rest is released under the Expat license
(license (list license:expat license:bsd-3))))
+(define-public idr
+ (package
+ (name "idr")
+ (version "2.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/nboley/idr/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (python-version (string-take (string-take-right
+ (assoc-ref inputs "python") 5) 3))
+ (path (string-join
+ (map (lambda (name)
+ (string-append (assoc-ref inputs name)
+ "/lib/python" python-version
+ "/site-packages"))
+ '("python-scipy"
+ "python-numpy"
+ "python-matplotlib"))
+ ":")))
+ (wrap-program (string-append out "/bin/idr")
+ `("PYTHONPATH" ":" prefix (,path))))
+ #t)))))
+ (inputs
+ `(("python-scipy" ,python-scipy)
+ ("python-numpy" ,python-numpy)
+ ("python-matplotlib" ,python-matplotlib)))
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-setuptools" ,python-setuptools)))
+ (home-page "https://github.com/nboley/idr")
+ (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
+ (description
+ "The IDR (Irreproducible Discovery Rate) framework is a unified approach
+to measure the reproducibility of findings identified from replicate
+experiments and provide highly stable thresholds based on reproducibility.")
+ (license license:gpl3+)))
+
(define-public macs
(package
(name "macs")
--
2.1.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] Add idr.
2015-06-17 10:51 ` Ricardo Wurmus
@ 2015-06-21 21:13 ` Ludovic Courtès
0 siblings, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2015-06-21 21:13 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> You are right. Is the attached patch better?
>
> From 37db5b51fe4a09496e149d59b64aa0b69ae42fd1 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 16 Jun 2015 11:33:26 +0200
> Subject: [PATCH] gnu: Add idr.
>
> * gnu/packages/bioinformatics.scm (idr): New variable.
Yes, please push!
Thank you,
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
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2015-06-16 9:37 [PATCH] Add idr Ricardo Wurmus
2015-06-16 15:36 ` Ludovic Courtès
2015-06-17 10:51 ` Ricardo Wurmus
2015-06-21 21:13 ` Ludovic Courtès
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