* [bug#27376] [PATCH] gnu: Add kentutils.
@ 2017-06-15 14:10 Ricardo Wurmus
2017-06-22 21:57 ` Kei Kebreau
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2017-06-15 14:10 UTC (permalink / raw)
To: 27376; +Cc: Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kentutils): New variable.
---
gnu/packages/bioinformatics.scm | 115 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 115 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 22a81f160..1f71f80ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -50,6 +50,7 @@
#:use-module (gnu packages cpio)
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
+ #:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
@@ -84,6 +85,7 @@
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
@@ -9496,3 +9498,116 @@ correct interaction matrices, identify adn compare the so-called
interaction matrices, and finally, extract structural properties from the
models. TADbit is complemented by TADkit for visualizing 3D models.")
(license license:gpl3+)))
+
+(define-public kentutils
+ (package
+ (name "kentutils")
+ ;; 302.1.0 is out, but the only difference is the inclusion of
+ ;; pre-built binaries.
+ (version "302.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
+ (modules '((guix build utils)
+ (srfi srfi-26)
+ (ice-9 ftw)))
+ (snippet
+ '(begin
+ ;; Only the contents of the specified directories are free
+ ;; for all uses, so we remove the rest. "hg/autoSql" and
+ ;; "hg/autoXml" are nominally free, but they depend on a
+ ;; library that is built from the sources in "hg/lib",
+ ;; which is nonfree.
+ (let ((free (list "." ".."
+ "utils" "lib" "inc" "tagStorm"
+ "parasol" "htslib"))
+ (directory? (lambda (file)
+ (eq? 'directory (stat:type (stat file))))))
+ (for-each (lambda (file)
+ (and (directory? file)
+ (delete-file-recursively file)))
+ (map (cut string-append "src/" <>)
+ (scandir "src"
+ (lambda (file)
+ (not (member file free)))))))
+ ;; Only make the utils target, not the userApps target,
+ ;; because that requires libraries we won't build.
+ (substitute* "Makefile"
+ ((" userApps") " utils"))
+ ;; Only build libraries that are free.
+ (substitute* "src/makefile"
+ (("DIRS =.*") "DIRS =\n")
+ (("cd jkOwnLib.*") "")
+ ((" hgLib") "")
+ (("cd hg.*") ""))
+ (substitute* "src/utils/makefile"
+ ;; These tools depend on "jkhgap.a", which is part of the
+ ;; nonfree "src/hg/lib" directory.
+ (("raSqlQuery") "")
+ (("pslLiftSubrangeBlat") "")
+
+ ;; Do not build UCSC tools, which may require nonfree
+ ;; components.
+ (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `( ;; There is no global test target and the test target for
+ ;; individual tools depends on input files that are not
+ ;; included.
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-paths
+ (lambda _
+ (substitute* "Makefile"
+ (("/bin/echo") (which "echo")))
+ #t))
+ (add-after 'unpack 'prepare-samtabix
+ (lambda* (#:key inputs #:allow-other-keys)
+ (copy-recursively (assoc-ref inputs "samtabix")
+ "samtabix")
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (copy-recursively "bin" bin))
+ #t)))))
+ (native-inputs
+ `(("samtabix"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "http://genome-source.cse.ucsc.edu/samtabix.git")
+ (commit "10fd107909c1ac4d679299908be4262a012965ba")))
+ (sha256
+ (base32
+ "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("tcsh" ,tcsh)
+ ("perl" ,perl)
+ ("libpng" ,libpng)
+ ("mysql" ,mysql)
+ ("openssl" ,openssl)))
+ (home-page "http://genome.cse.ucsc.edu/index.html")
+ (synopsis "Assorted bioinformatics utilities")
+ (description "This package provides the kentUtils, a selection of
+bioinformatics utilities used in combination with the UCSC genome
+browser.")
+ ;; Only a subset of the sources are released under a non-copyleft
+ ;; free software license. All other sources are removed in a
+ ;; snippet. See this bug report for an explanation of how the
+ ;; license statements apply:
+ ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
+ (license (license:non-copyleft
+ "http://genome.ucsc.edu/license/"
+ "The contents of this package are free for all uses."))))
--
2.13.0
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [bug#27376] [PATCH] gnu: Add kentutils.
2017-06-15 14:10 [bug#27376] [PATCH] gnu: Add kentutils Ricardo Wurmus
@ 2017-06-22 21:57 ` Kei Kebreau
2017-06-23 6:10 ` bug#27376: " Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Kei Kebreau @ 2017-06-22 21:57 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: 27376
[-- Attachment #1: Type: text/plain, Size: 6299 bytes --]
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> * gnu/packages/bioinformatics.scm (kentutils): New variable.
> ---
> gnu/packages/bioinformatics.scm | 115 ++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 115 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 22a81f160..1f71f80ae 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -50,6 +50,7 @@
> #:use-module (gnu packages cpio)
> #:use-module (gnu packages curl)
> #:use-module (gnu packages documentation)
> + #:use-module (gnu packages databases)
> #:use-module (gnu packages datastructures)
> #:use-module (gnu packages file)
> #:use-module (gnu packages flex)
> @@ -84,6 +85,7 @@
> #:use-module (gnu packages readline)
> #:use-module (gnu packages ruby)
> #:use-module (gnu packages serialization)
> + #:use-module (gnu packages shells)
> #:use-module (gnu packages statistics)
> #:use-module (gnu packages swig)
> #:use-module (gnu packages tbb)
> @@ -9496,3 +9498,116 @@ correct interaction matrices, identify adn compare the so-called
> interaction matrices, and finally, extract structural properties from the
> models. TADbit is complemented by TADkit for visualizing 3D models.")
> (license license:gpl3+)))
> +
> +(define-public kentutils
> + (package
> + (name "kentutils")
> + ;; 302.1.0 is out, but the only difference is the inclusion of
> + ;; pre-built binaries.
> + (version "302.0.0")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
> + "archive/v" version ".tar.gz"))
> + (file-name (string-append name "-" version ".tar.gz"))
> + (sha256
> + (base32
> + "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
> + (modules '((guix build utils)
> + (srfi srfi-26)
> + (ice-9 ftw)))
> + (snippet
> + '(begin
> + ;; Only the contents of the specified directories are free
> + ;; for all uses, so we remove the rest. "hg/autoSql" and
> + ;; "hg/autoXml" are nominally free, but they depend on a
> + ;; library that is built from the sources in "hg/lib",
> + ;; which is nonfree.
> + (let ((free (list "." ".."
> + "utils" "lib" "inc" "tagStorm"
> + "parasol" "htslib"))
> + (directory? (lambda (file)
> + (eq? 'directory (stat:type (stat file))))))
> + (for-each (lambda (file)
> + (and (directory? file)
> + (delete-file-recursively file)))
> + (map (cut string-append "src/" <>)
> + (scandir "src"
> + (lambda (file)
> + (not (member file free)))))))
> + ;; Only make the utils target, not the userApps target,
> + ;; because that requires libraries we won't build.
> + (substitute* "Makefile"
> + ((" userApps") " utils"))
> + ;; Only build libraries that are free.
> + (substitute* "src/makefile"
> + (("DIRS =.*") "DIRS =\n")
> + (("cd jkOwnLib.*") "")
> + ((" hgLib") "")
> + (("cd hg.*") ""))
> + (substitute* "src/utils/makefile"
> + ;; These tools depend on "jkhgap.a", which is part of the
> + ;; nonfree "src/hg/lib" directory.
> + (("raSqlQuery") "")
> + (("pslLiftSubrangeBlat") "")
> +
> + ;; Do not build UCSC tools, which may require nonfree
> + ;; components.
> + (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
> + #t))))
> + (build-system gnu-build-system)
> + (arguments
> + `( ;; There is no global test target and the test target for
> + ;; individual tools depends on input files that are not
> + ;; included.
> + #:tests? #f
> + #:phases
> + (modify-phases %standard-phases
> + (add-after 'unpack 'fix-paths
> + (lambda _
> + (substitute* "Makefile"
> + (("/bin/echo") (which "echo")))
> + #t))
> + (add-after 'unpack 'prepare-samtabix
> + (lambda* (#:key inputs #:allow-other-keys)
> + (copy-recursively (assoc-ref inputs "samtabix")
> + "samtabix")
> + #t))
> + (delete 'configure)
> + (replace 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let ((bin (string-append (assoc-ref outputs "out")
> + "/bin")))
> + (copy-recursively "bin" bin))
> + #t)))))
> + (native-inputs
> + `(("samtabix"
> + ,(origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "http://genome-source.cse.ucsc.edu/samtabix.git")
> + (commit "10fd107909c1ac4d679299908be4262a012965ba")))
> + (sha256
> + (base32
> + "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
> + (inputs
> + `(("zlib" ,zlib)
> + ("tcsh" ,tcsh)
> + ("perl" ,perl)
> + ("libpng" ,libpng)
> + ("mysql" ,mysql)
> + ("openssl" ,openssl)))
> + (home-page "http://genome.cse.ucsc.edu/index.html")
> + (synopsis "Assorted bioinformatics utilities")
> + (description "This package provides the kentUtils, a selection of
> +bioinformatics utilities used in combination with the UCSC genome
> +browser.")
> + ;; Only a subset of the sources are released under a non-copyleft
> + ;; free software license. All other sources are removed in a
> + ;; snippet. See this bug report for an explanation of how the
> + ;; license statements apply:
> + ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
> + (license (license:non-copyleft
> + "http://genome.ucsc.edu/license/"
> + "The contents of this package are free for all uses."))))
LGTM.
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^ permalink raw reply [flat|nested] 3+ messages in thread
* bug#27376: [PATCH] gnu: Add kentutils.
2017-06-22 21:57 ` Kei Kebreau
@ 2017-06-23 6:10 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2017-06-23 6:10 UTC (permalink / raw)
To: Kei Kebreau; +Cc: 27376-done
Kei Kebreau <kei@openmailbox.org> writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> * gnu/packages/bioinformatics.scm (kentutils): New variable.
[…]
> LGTM.
Thanks. Pushed to master with commit 94820951d.
-- Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
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2017-06-15 14:10 [bug#27376] [PATCH] gnu: Add kentutils Ricardo Wurmus
2017-06-22 21:57 ` Kei Kebreau
2017-06-23 6:10 ` bug#27376: " Ricardo Wurmus
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