Hi Guix, pbtranscript-tofu has a few more dependencies that the install script didn't check for. The four patches add packages for as yet unpackaged dependencies (python-decorator and python-networkx), remove even more pre-built stuff from the pbtranscript-tofu tarball, and finally add all missing inputs.
~~ Ricardo
>From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de> Date: Tue, 31 Mar 2015 12:34:37 +0200 Subject: [PATCH 1/4] gnu: Add python-decorator. * gnu/packages/python.scm (python-decorator, python2-decorator): New variables. --- gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 23afec7..f7eb478 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2837,6 +2837,34 @@ PNG, PostScript, PDF, and SVG file output.") (define-public python2-cairocffi (package-with-python2 python-cairocffi)) +(define-public python-decorator + (package + (name "python-decorator") + (version "3.4.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/d/decorator/decorator-" + version ".tar.gz")) + (sha256 + (base32 "0i2bnlkh0p9gs76hb28mafandcrig2fmv56w9ai6mshxwqn0083k")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; no test target + (native-inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "http://pypi.python.org/pypi/decorator/") + (synopsis "Python module to simplify usage of decorators") + (description + "The aim of the decorator module is to simplify the usage of decorators +for the average programmer, and to popularize decorators usage giving examples +of useful decorators, such as memoize, tracing, redirecting_stdout, locked, +etc. The core of this module is a decorator factory.") + (license license:expat))) + +(define-public python2-decorator + (package-with-python2 python-decorator)) + (define-public python-ipython (package (name "python-ipython") -- 2.1.0
>From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de> Date: Tue, 31 Mar 2015 12:35:09 +0200 Subject: [PATCH 2/4] gnu: Add python-networkx. * gnu/packages/python.scm (python-networkx, python2-networkx): New variables. --- gnu/packages/python.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f7eb478..c5cae6d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3335,6 +3335,35 @@ interfaces in an easy and portable manner.") (define-public python2-netifaces (package-with-python2 python-netifaces)) +(define-public python-networkx + (package + (name "python-networkx") + (version "1.9.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/n/networkx/networkx-" + version ".tar.gz")) + (sha256 + (base32 "0n8wy0yq1kmdq4wh68mlhwhkndvwzx48lg41a1z0sxxms0wfp033")))) + (build-system python-build-system) + ;; python-decorator is needed at runtime + (propagated-inputs + `(("python-decorator" ,python-decorator))) + (native-inputs + `(("python-setuptools" ,python-setuptools) + ("python-nose" ,python-nose))) + (home-page "http://networkx.github.io/") + (synopsis "Python module for creating and manipulating graphs and networks") + (description + "NetworkX is a Python package for the creation, manipulation, and study +of the structure, dynamics, and functions of complex networks.") + (license bsd-3))) + +(define-public python2-networkx + (package-with-python2 python-networkx)) + (define-public snakemake (package (name "snakemake") -- 2.1.0
>From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de> Date: Tue, 31 Mar 2015 12:37:31 +0200 Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries. * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete "build" directory and any shared objects after unpacking. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 93dc542..f124732 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -830,12 +830,15 @@ files and writing bioinformatics applications.") (chdir "pbtranscript-tofu/pbtranscript/") ;; Delete clutter (delete-file-recursively "dist/") + (delete-file-recursively "build/") (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") + (for-each delete-file + (find-files "." "\\.so")) ;; files should be writable for install phase (for-each (lambda (f) (chmod f #o755)) (find-files "." "\\.py"))) -- 2.1.0
>From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de> Date: Tue, 31 Mar 2015 13:46:27 +0200 Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs. * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing runtime inputs. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f124732..76dd2cd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -847,6 +847,8 @@ files and writing bioinformatics applications.") `(("python-cython" ,python2-cython) ("python-numpy" ,python2-numpy) ("python-bx-python" ,python2-bx-python) + ("python-networkx" ,python2-networkx) + ("python-scipy" ,python2-scipy) ("python-pbcore" ,python2-pbcore))) (native-inputs `(("python-nose" ,python2-nose) -- 2.1.0