From da5ebd1007488209ba82ef02f0cb7f097f2b9106 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:18:26 +0100 Subject: gnu: python-biom-format: Fix tests. * gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3d84a44e4c..5f56551526 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -562,6 +562,8 @@ Python.") ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py))) + (native-inputs + `(("python-nose" ,python-nose))) (home-page "http://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description -- cgit v1.2.3 From d281be18bca2437ff27f8c045c5dd5a3e5b77e57 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 04:26:32 +0100 Subject: gnu: clipper: Fix test dependency. * gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f56551526..3a7bffba79 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1562,6 +1562,7 @@ databases.") ("python-scipy" ,python2-scipy))) (native-inputs `(("python-mock" ,python2-mock) ; for tests + ("python-nose" ,python2-nose) ; for tests ("python-pytz" ,python2-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") -- cgit v1.2.3 From aaffb9c97b8daae7dd81547e8b808ac73fd65f4f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 04:27:35 +0100 Subject: gnu: deeptools: Fix test dependency. * gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a7bffba79..e160015b1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2002,6 +2002,7 @@ trees (phylogenies) and characters.") ("python-pybigwig" ,python2-pybigwig))) (native-inputs `(("python-mock" ,python2-mock) ;for tests + ("python-nose" ,python2-nose) ;for tests ("python-pytz" ,python2-pytz))) ;for tests (home-page "https://github.com/fidelram/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") -- cgit v1.2.3 From 1c10a1d75c78afc85f5709743b1ac5f83e1897f4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:08:57 +0100 Subject: gnu: idr: Disable tests. * gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f. --- gnu/packages/bioinformatics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e160015b1f..fc75fd1abd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2879,7 +2879,8 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; FIXME: "ImportError: No module named 'utility'" + #:phases (modify-phases %standard-phases (add-after 'install 'wrap-program -- cgit v1.2.3 From b7a820fc97485a7bdf7703d3b627871d6a6be6c6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:11:20 +0100 Subject: gnu: idr: Correct inputs. * gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ... [propagated-inputs]: ... to here. Add python-sympy. --- gnu/packages/bioinformatics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc75fd1abd..a2191d060b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2900,8 +2900,9 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") (wrap-program (string-append out "/bin/idr") `("PYTHONPATH" ":" prefix (,path)))) #t))))) - (inputs + (propagated-inputs `(("python-scipy" ,python-scipy) + ("python-sympy" ,python-sympy) ("python-numpy" ,python-numpy) ("python-matplotlib" ,python-matplotlib))) (native-inputs -- cgit v1.2.3 From 14386fc7d9192b35a81dedb7616a44651807ee19 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:16:39 +0100 Subject: gnu: idr: Remove explicit wrapper. This is now done implicitly. * gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases. --- gnu/packages/bioinformatics.scm | 22 +--------------------- 1 file changed, 1 insertion(+), 21 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2191d060b..3fb9bbc35d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2879,27 +2879,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:tests? #f ; FIXME: "ImportError: No module named 'utility'" - #: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))))) + `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'" (propagated-inputs `(("python-scipy" ,python-scipy) ("python-sympy" ,python-sympy) -- cgit v1.2.3 From 0d9087597467c3e34cf614a5475bfb0ea75b133b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:28:49 +0100 Subject: gnu: multiqc: Fix test dependencies. * gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3fb9bbc35d..e37226b275 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7843,6 +7843,8 @@ replacement for strverscmp.") (base32 "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy")))) (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) -- cgit v1.2.3 From cdc2bb50b29422e8edfb00cabb5edd632f6ebe07 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 18:15:47 +0100 Subject: gnu: pbtranscript-tofu: Disable tests. * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e37226b275..50b0bfaa03 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3572,6 +3572,9 @@ the phenotype as it models the data.") (build-system python-build-system) (arguments `(#:python ,python-2 + ;; FIXME: Tests fail with "No such file or directory: + ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" + #:tests? #f #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-directory -- cgit v1.2.3 From 1885bb0c08e943a2e0e37c5c0a83473c8af904d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 21 Feb 2017 18:28:21 +0100 Subject: gnu: python-dendropy: Fix failing tests. * gnu/packages/patches/python-dendropy-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 3 +- .../patches/python-dendropy-fix-tests.patch | 41 ++++++++++++++++++++++ 3 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-dendropy-fix-tests.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 63eb56cc51..899dc06b8e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -853,6 +853,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-3-search-paths.patch \ %D%/packages/patches/python-3.4-fix-tests.patch \ %D%/packages/patches/python-3.5-fix-tests.patch \ + %D%/packages/patches/python-dendropy-fix-tests.patch \ %D%/packages/patches/python-file-double-encoding-bug.patch \ %D%/packages/patches/python-fix-tests.patch \ %D%/packages/patches/python-parse-too-many-fields.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a1738b936..de6186de27 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1981,7 +1981,8 @@ accessing bigWig files.") (uri (pypi-uri "DendroPy" version)) (sha256 (base32 - "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) + "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) + (patches (search-patches "python-dendropy-fix-tests.patch")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") diff --git a/gnu/packages/patches/python-dendropy-fix-tests.patch b/gnu/packages/patches/python-dendropy-fix-tests.patch new file mode 100644 index 0000000000..30ab618ff1 --- /dev/null +++ b/gnu/packages/patches/python-dendropy-fix-tests.patch @@ -0,0 +1,41 @@ +This patch fixes two test failures. It was downloaded from: +https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453 + +From 93f984bba7a6c588a28ca87f4e557ce283809453 Mon Sep 17 00:00:00 2001 +From: jeetsukumaran +Date: Tue, 21 Feb 2017 16:41:01 -0500 +Subject: [PATCH] Update to Python 3 container and iteration semantics + +--- + dendropy/dataio/newickreader.py | 3 ++- + dendropy/datamodel/treemodel.py | 3 +++ + 2 files changed, 5 insertions(+), 1 deletion(-) + +diff --git a/dendropy/dataio/newickreader.py b/dendropy/dataio/newickreader.py +index 6dcf3c5..f978729 100644 +--- a/dendropy/dataio/newickreader.py ++++ b/dendropy/dataio/newickreader.py +@@ -303,7 +303,8 @@ def tree_iter(self, + taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol) + yield tree + if tree is None: +- raise StopIteration ++ # raise StopIteration ++ return + + def _read(self, + stream, +diff --git a/dendropy/datamodel/treemodel.py b/dendropy/datamodel/treemodel.py +index 0ecfe31..73146f0 100644 +--- a/dendropy/datamodel/treemodel.py ++++ b/dendropy/datamodel/treemodel.py +@@ -772,6 +772,9 @@ def __hash__(self): + def __eq__(self, other): + return self is other + ++ def __lt__(self, other): ++ return id(self) < id(other) ++ + ########################################################################### + ### Basic Structure + -- cgit v1.2.3 From 2bb12f5a68f6547b3de295c22c2886aaa0415e47 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 15:30:03 +0100 Subject: gnu: ribodiff: Fix test failure. * gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK and PYTHON2-NOSE. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index de6186de27..bdcb5a4010 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -499,6 +499,9 @@ provides the Ribotaper pipeline.") ("python-matplotlib" ,python2-matplotlib) ("python-scipy" ,python2-scipy) ("python-statsmodels" ,python2-statsmodels))) + (native-inputs + `(("python-mock" ,python2-mock) + ("python-nose" ,python2-nose))) (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein -- cgit v1.2.3 From 48d66a9c99a9cc8e9c27c9608da7e8729be206b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 27 Feb 2017 18:43:12 +0100 Subject: gnu: bamtools: Update to 2.4.1. * gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a448b51c6c..1810773de4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -238,7 +238,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (define-public bamtools (package (name "bamtools") - (version "2.3.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (string-append @@ -247,7 +247,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018")))) + "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target -- cgit v1.2.3 From a9f754d73320703c257a29f926aae77a23ef66db Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 2 Mar 2017 21:13:39 +1000 Subject: gnu: diamond: Update to 0.8.36. * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1810773de4..0fc8c0483e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus -;;; Copyright © 2015, 2016 Ben Woodcroft +;;; Copyright © 2015, 2016, 2017 Ben Woodcroft ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Roel Janssen @@ -2047,7 +2047,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.34") + (version "0.8.36") (source (origin (method url-fetch) (uri (string-append @@ -2056,7 +2056,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jvr34g346gbz7z1zb9bs0vplivm9p4cxk0lbzklvdpa7g236p39")))) + "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit v1.2.3