From b62715aa82cd884936124f2060e718957721138b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 14:10:23 +0200 Subject: gnu: snakemake: Update to 5.2.0. * gnu/packages/python.scm (snakemake): Update to 5.2.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fc1ef3eb2a..f20de13720 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5139,13 +5139,13 @@ of the structure, dynamics, and functions of complex networks.") (define-public snakemake (package (name "snakemake") - (version "4.4.0") + (version "5.2.0") (source (origin (method url-fetch) (uri (pypi-uri "snakemake" version)) (sha256 - (base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv")))) + (base32 "0a1i5v5qxbmmpznp7my9nva8y7pxp8pjrwk2gxgisdskg35sq8s1")))) (build-system python-build-system) (arguments ;; TODO: Package missing test dependencies. -- cgit v1.3 From 216a72a95738d6d643094f156000cbc006cd79f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 15:07:12 +0200 Subject: gnu: Add python-datrie. * gnu/packages/python.scm (python-datrie): New variable. --- gnu/packages/python.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f20de13720..1422ad26a3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5136,6 +5136,30 @@ of the structure, dynamics, and functions of complex networks.") (define-public python2-networkx2 (package-with-python2 python-networkx2)) +(define-public python-datrie + (package + (name "python-datrie") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "datrie" version)) + (sha256 + (base32 + "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs")))) + (build-system python-build-system) + (native-inputs + `(("python-cython" ,python-cython) + ("python-hypothesis" ,python-hypothesis) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://github.com/kmike/datrie") + (synopsis "Fast, efficiently stored trie for Python") + (description + "This package provides a fast, efficiently stored trie implementation for +Python.") + (license license:lgpl2.1+))) + (define-public snakemake (package (name "snakemake") -- cgit v1.3 From 269f100330cf92afdc911bbd7db0644719d6dc3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 15:07:26 +0200 Subject: gnu: snakemake: Add missing dependencies. * gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-datrie, python-docutils, python-jinja2, python-jsonschema, and python-networkx. --- gnu/packages/python.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1422ad26a3..a6e3ebb9d6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5191,6 +5191,11 @@ Python.") ("python-requests" ,python-requests) ("python-appdirs" ,python-appdirs) ("python-configargparse" ,python-configargparse) + ("python-datrie" ,python-datrie) + ("python-docutils" ,python-docutils) + ("python-jinja2" ,python-jinja2) + ("python-jsonschema" ,python-jsonschema) + ("python-networkx" ,python-networkx) ("python-pyyaml" ,python-pyyaml) ("python-ratelimiter" ,python-ratelimiter))) (home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home") -- cgit v1.3 From ed2dfe3955f0144bc858c66fdb751f51e9bd84fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 15:13:56 +0200 Subject: gnu: Add snakemake-4. * gnu/packages/python.scm (snakemake-4): New variable. * gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq, pigx-chipseq)[inputs]: Use it. --- gnu/packages/bioinformatics.scm | 8 ++++---- gnu/packages/python.scm | 18 ++++++++++++++++++ 2 files changed, 22 insertions(+), 4 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 73cca16717..bb0e8c73c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12837,7 +12837,7 @@ once. This package provides tools to perform Drop-seq analyses.") #t))))) (inputs `(("gzip" ,gzip) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("fastqc" ,fastqc) ("multiqc" ,multiqc) ("star" ,star) @@ -12931,7 +12931,7 @@ expression report comparing samples in an easily configurable manner.") ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -12992,7 +12992,7 @@ in an easily configurable manner.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13041,7 +13041,7 @@ methylation and segmentation.") ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc-1) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a6e3ebb9d6..e9fb9f529f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5206,6 +5206,24 @@ providing a clean and modern domain specific specification language (DSL) in Python style, together with a fast and comfortable execution environment.") (license license:expat))) +;; This is currently needed for the pigx-* packages. +(define-public snakemake-4 + (package (inherit snakemake) + (version "4.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "snakemake" version)) + (sha256 + (base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv")))) + (propagated-inputs + `(("python-wrapt" ,python-wrapt) + ("python-requests" ,python-requests) + ("python-appdirs" ,python-appdirs) + ("python-configargparse" ,python-configargparse) + ("python-pyyaml" ,python-pyyaml) + ("python-ratelimiter" ,python-ratelimiter))))) + (define-public python-pyqrcode (package (name "python-pyqrcode") -- cgit v1.3 From 6465497fb9a8980bc010ec8f68b320dc1a73b5cb Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 17 Jul 2018 21:13:38 +0100 Subject: gnu: Remove duplicated python-pafy. It was first added in 02f8f804f0242df885311715412a1e3ee5436f3b, then again in 2dd12924cf4a30a96262b6d392fcde58c9f10d4b. * gnu/packages/python.scm (python-pafy): Remove duplicated package definition. --- gnu/packages/python.scm | 24 ------------------------ 1 file changed, 24 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e9fb9f529f..d4448f23ad 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1747,30 +1747,6 @@ matching them against a list of media-ranges.") `(#:tests? #f ,@(package-arguments python2-funcsigs))))) -(define-public python-pafy - (package - (name "python-pafy") - (version "0.5.3.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pafy" version)) - (sha256 - (base32 - "1a7dxi95m1043rxx1r5x3ngb66nwlq6aqcasyqqjzmmmjps4zrim")))) - (build-system python-build-system) - (arguments - `(#:tests? #f)) ; Currently pafy can not find itself in the tests - (propagated-inputs - ;; Youtube-dl is a python package which is imported in the file - ;; "backend_youtube_dl.py", therefore it needs to be propagated. - `(("youtube-dl" ,youtube-dl))) - (home-page "https://np1.github.io/pafy/") - (synopsis "Retrieve YouTube content and metadata") - (description - "@code{pafy} is a python library to retrieve YouTube content and metadata.") - (license license:lgpl3+))) - (define-public python-py (package (name "python-py") -- cgit v1.3