* [PATCH] Add pbtranscript-tofu.
@ 2015-03-20 13:49 Ricardo Wurmus
2015-03-24 9:23 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-03-20 13:49 UTC (permalink / raw)
To: guix-devel
[-- Attachment #1: Type: text/plain, Size: 799 bytes --]
Hi Guix,
attached is a patch to add a couple of transcriptome analysis scripts.
I had to use the git downloader because the releases are unusable: they
are really old and only contain the scripts but no longer the setup.py
script.
The git clone also isn't that nice; I had to delete some clutter after
unpacking and fix the permissions on the python scripts or else
installation would fail.
About the name: "pbtranscript(-tofu)" is the correct name, whereas
"cDNA_primer" is not, even though the repository is named "cDNA_primer".
This patch depends on three other packages:
- python2-pbcore:
http://lists.gnu.org/archive/html/guix-devel/2015-03/msg00573.html
- python2-h5py:
http://lists.gnu.org/archive/html/guix-devel/2015-03/msg00532.html
- python2-bx-python:
attached
~~ Ricardo
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-python2-bx-python.patch --]
[-- Type: text/x-patch, Size: 2182 bytes --]
From 39f77a513b2505d2a9658f6f9ed40f24a6b93dfd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 18 Mar 2015 14:39:42 +0100
Subject: [PATCH 1/2] gnu: Add python2-bx-python.
* gnu/packages/bioinformatics.scm (python2-bx-python): 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 a8592d0..4ab6054 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -289,6 +289,41 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
(license license:gpl3+)))
+(define-public python2-bx-python
+ (package
+ (name "python2-bx-python")
+ (version "0.7.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* "setup.py"
+ ;; remove dependency on outdated "distribute" module
+ (("^from distribute_setup import use_setuptools") "")
+ (("^use_setuptools\\(\\)") "")))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ;tests fail because test data are not included
+ #:python ,python-2))
+ (inputs
+ `(("python-numpy" ,python2-numpy)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("python-nose" ,python2-nose)
+ ("python-setuptools" ,python2-setuptools)))
+ (home-page "http://bitbucket.org/james_taylor/bx-python/")
+ (synopsis "Tools for manipulating biological data")
+ (description
+ "bx-python provides tools for manipulating biological data, particularly
+multiple sequence alignments.")
+ (license license:expat)))
+
(define-public clipper
(package
(name "clipper")
--
2.1.0
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-Add-pbtranscript-tofu.patch --]
[-- Type: text/x-patch, Size: 3428 bytes --]
From 42c865d2c29b7c68e81580de98997266112d6cd9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Mar 2015 14:36:38 +0100
Subject: [PATCH 2/2] gnu: Add pbtranscript-tofu.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
---
gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4ab6054..46ce4f4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -20,6 +20,7 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system python)
@@ -738,6 +739,59 @@ that a read originated from a particular isoform.")
files and writing bioinformatics applications.")
(license license:bsd-3)))
+(define-public pbtranscript-tofu
+ (package
+ (name "pbtranscript-tofu")
+ (version "0.4.1-c7bbd5472")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/PacificBiosciences/cDNA_primer.git")
+ (commit "c7bbd54720df578777743d687ceaf6b4f6d4919e")))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ ;; With standard flags, the install phase attempts to create a zip'd
+ ;; egg file, and fails with an error: 'ZIP does not support timestamps
+ ;; before 1980'
+ #:configure-flags '("--single-version-externally-managed"
+ "--record=pbtranscript-tofu.txt")
+ #:phases
+ (alist-cons-after
+ 'unpack 'enter-directory-and-clean-up
+ (lambda _
+ (chdir "pbtranscript-tofu/pbtranscript/")
+ ;; Delete clutter
+ (delete-file-recursively "dist/")
+ (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
+ (delete-file-recursively "pbtools.pbtranscript.egg-info")
+ (delete-file "Cython-0.20.1.tar.gz")
+ (delete-file "setuptools_cython-0.2.1-py2.7.egg")
+ (delete-file "setuptools_cython-0.2.1.tar.gz")
+ (delete-file "setup.cfg")
+ ;; files should be writable for install phase
+ (for-each (lambda (f) (chmod f #o755))
+ (find-files "." "\\.py")))
+ %standard-phases)))
+ (inputs
+ `(("python-cython" ,python2-cython)
+ ("python-numpy" ,python2-numpy)
+ ("python-bx-python" ,python2-bx-python)
+ ("python-pbcore" ,python2-pbcore)))
+ (native-inputs
+ `(("python-nose" ,python2-nose)
+ ("python-setuptools" ,python2-setuptools)))
+ (home-page "https://github.com/PacificBiosciences/cDNA_primer")
+ (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
+ (description
+ "pbtranscript-tofu contains scripts to analyze transcriptome data
+generated using the PacBio Iso-Seq protocol.")
+ (license license:bsd-3)))
+
(define-public rseqc
(package
(name "rseqc")
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add pbtranscript-tofu.
2015-03-20 13:49 [PATCH] Add pbtranscript-tofu Ricardo Wurmus
@ 2015-03-24 9:23 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-03-24 9:23 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 39f77a513b2505d2a9658f6f9ed40f24a6b93dfd Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 18 Mar 2015 14:39:42 +0100
> Subject: [PATCH 1/2] gnu: Add python2-bx-python.
>
> * gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
LGTM.
> From 42c865d2c29b7c68e81580de98997266112d6cd9 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Mar 2015 14:36:38 +0100
> Subject: [PATCH 2/2] gnu: Add pbtranscript-tofu.
>
> * gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
[...]
> + (version "0.4.1-c7bbd5472")
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/PacificBiosciences/cDNA_primer.git")
> + (commit "c7bbd54720df578777743d687ceaf6b4f6d4919e")))
To avoid mistakes in the future, I would do:
(let ((commit "c7bbd5472"))
(package
(version (string-append "0.4.1." commit))
(source (origin ...
(commit commit)))
;; ...
))
Also, I think 0.4.1.c7bbd5472 is slightly nicer than 0.4.1-c7bbd5472.
Other than that LGTM.
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 2+ messages in thread
end of thread, other threads:[~2015-03-24 9:23 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2015-03-20 13:49 [PATCH] Add pbtranscript-tofu Ricardo Wurmus
2015-03-24 9:23 ` Ludovic Courtès
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.