From c9a656a5d009c5cb19591a83fd759e00bcb14c14 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 23 Oct 2020 12:11:41 +0200 Subject: gnu: imp: Update to 2.13.0. * gnu/packages/bioinformatics.scm (imp): Update to 2.13.0. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fefca80e9e..41d92401ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10954,7 +10954,7 @@ programs for inferring phylogenies (evolutionary trees).") (define-public imp (package (name "imp") - (version "2.6.2") + (version "2.13.0") (source (origin (method url-fetch) @@ -10962,7 +10962,7 @@ programs for inferring phylogenies (evolutionary trees).") version "/download/imp-" version ".tar.gz")) (sha256 (base32 - "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) + "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj")))) (build-system cmake-build-system) (arguments `(;; FIXME: Some tests fail because they produce warnings, others fail @@ -10974,6 +10974,7 @@ programs for inferring phylogenies (evolutionary trees).") ("swig" ,swig) ("hdf5" ,hdf5) ("fftw" ,fftw) + ("eigen" ,eigen) ("python" ,python-2))) (propagated-inputs `(("python2-numpy" ,python2-numpy) -- cgit v1.2.3 From f40add4dbb45a5a87fd5213e23e7ab0cc77c008e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Oct 2020 11:41:27 +0100 Subject: gnu: Update htslib to 1.11. * gnu/packages/bioinformatics.scm (htslib): Update to 1.11. --- 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 41d92401ad..09216f6a8d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4215,7 +4215,7 @@ performance.") (define-public htslib (package (name "htslib") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) (uri (string-append @@ -4223,7 +4223,7 @@ performance.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))) + "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng")))) (build-system gnu-build-system) ;; Let htslib translate "gs://" and "s3://" to regular https links with ;; "--enable-gcs" and "--enable-s3". For these options to work, we also -- cgit v1.2.3 From 04a49b414303c329032f74de67541cc39d2271c6 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Oct 2020 11:57:16 +0100 Subject: gnu: Update bcftools to 1.11. * gnu/packages/bioinformatics.scm (bcftools): Update to 1.11. --- 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 09216f6a8d..a428ba1fed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -313,7 +313,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" @@ -321,11 +321,11 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.11") #t)))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From bcbd536e3f22e7bcce6ef535171f4257c79d2f0c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Oct 2020 11:58:02 +0100 Subject: gnu: Update samtools to 1.11. * gnu/packages/bioinformatics.scm (samtools): Update to 1.11. --- 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 a428ba1fed..4c49b00252 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5613,7 +5613,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) @@ -5622,11 +5622,11 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.11") #t)))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From fa82adb5e0e613037eb0377f318b7fa1423bdeba Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 9 Nov 2020 10:31:08 +0200 Subject: gnu: macs: Update source, home-page URIs. * gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update URIs to new location. --- 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 4c49b00252..a456b2b12c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4470,7 +4470,7 @@ experiments.") ;; The PyPi tarball does not contain tests. (method git-fetch) (uri (git-reference - (url "https://github.com/taoliu/MACS") + (url "https://github.com/macs3-project/MACS") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4489,7 +4489,7 @@ experiments.") `(("python-numpy" ,python-numpy))) (native-inputs `(("python-pytest" ,python-pytest))) - (home-page "https://github.com/taoliu/MACS/") + (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description "MACS is an implementation of a ChIP-Seq analysis algorithm for -- cgit v1.2.3 From 4dcd19d3ff143e7ef5ed1584a9ace65c348d1dfa Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 9 Nov 2020 10:36:14 +0200 Subject: gnu: macs: Update check phase. * gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check phase before using custom 'check phase. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a456b2b12c..010742b37b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4480,11 +4480,12 @@ experiments.") (arguments `(#:phases (modify-phases %standard-phases - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-v")))))) + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v")) + #t))))) (inputs `(("python-numpy" ,python-numpy))) (native-inputs -- cgit v1.2.3 From 4b3a535770b19d9c17196bd6e5c9337233d9fb92 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 9 Nov 2020 11:05:23 +0200 Subject: gnu: macs: Remove generated code. * gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove cython generated code. [native-inputs]: Add python-cython. --- gnu/packages/bioinformatics.scm | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 010742b37b..06972dee51 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4475,7 +4475,19 @@ experiments.") (file-name (git-file-name name version)) (sha256 (base32 - "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15")))) + "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15")) + (modules '((guix build utils))) + ;; Remove files generated by Cython + (snippet + '(begin + (for-each (lambda (file) + (let ((generated-file + (string-append (string-drop-right file 3) "c"))) + (when (file-exists? generated-file) + (delete-file generated-file)))) + (find-files "." "\\.pyx$")) + (delete-file "MACS2/IO/CallPeakUnitPrecompiled.c") + #t)))) (build-system python-build-system) (arguments `(#:phases @@ -4489,7 +4501,8 @@ experiments.") (inputs `(("python-numpy" ,python-numpy))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest))) (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description -- cgit v1.2.3 From 3ede804f6d4c38ff0b9a5705544a8c35f6827ff1 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 13 Nov 2020 11:28:43 +0100 Subject: gnu: Add htslib-1.9. * gnu/packages/bioinformatics.scm (htslib-1.9): New variable. --- gnu/packages/bioinformatics.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 06972dee51..ba86333fc3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4250,6 +4250,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public htslib-1.9 + (package (inherit htslib) + (name "htslib") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))))) + ;; This package should be removed once no packages rely upon it. (define htslib-1.3 (package -- cgit v1.2.3 From da4a38edad52f7bb5a8d41465d09f3f0197fd0b7 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 13 Nov 2020 11:29:20 +0100 Subject: gnu: Add samtools-1.9. * gnu/packages/bioinformatics.scm (samtools-1.9): New variable. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ba86333fc3..e047aebd1d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5699,6 +5699,31 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) +(define-public samtools-1.9 + (package (inherit samtools) + (name "samtools") + (version "1.9") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/samtools/samtools/" + version "/samtools-" version ".tar.bz2")) + (sha256 + (base32 + "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) + (inputs + `(("htslib" ,htslib-1.9) + ("ncurses" ,ncurses) + ("perl" ,perl) + ("python" ,python) + ("zlib" ,zlib))))) + (define-public samtools-0.1 ;; This is the most recent version of the 0.1 line of samtools. The input ;; and output formats differ greatly from that used and produced by samtools -- cgit v1.2.3 From c3232fcc7785abc1057a0d4b5b1832f1e39c9c1b Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 13 Nov 2020 11:29:38 +0100 Subject: gnu: bedtools: Use samtools-1.9. The build for bedtools with samtools 1.11 triggers a testsuite failure which is reported here: https://github.com/arq5x/bedtools2/issues/814 * gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e047aebd1d..8ad38ac498 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -437,7 +437,7 @@ computational cluster.") (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) + `(("samtools" ,samtools-1.9) ("zlib" ,zlib))) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") -- cgit v1.2.3 From ecc309c14202161eba28d498649a7ed53e89aaae Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 13 Nov 2020 16:14:01 +0100 Subject: gnu: Add bcftools-1.9. * gnu/packages/bioinformatics.scm (bcftools-1.9): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8ad38ac498..22da6ac3ff 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -354,6 +354,28 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. (license (list license:gpl3+ license:expat)))) +(define-public bcftools-1.9 + (package (inherit bcftools) + (name "bcftools") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/samtools/bcftools/" + "releases/download/" + version "/bcftools-" version ".tar.bz2")) + (sha256 + (base32 + "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) + (build-system gnu-build-system) + (native-inputs + `(("htslib" ,htslib-1.9) + ("perl" ,perl))))) + (define-public bedops (package (name "bedops") @@ -1955,7 +1977,7 @@ multiple sequence alignments.") ;; FIXME: tests keep timing out on some systems. (invoke "nosetests" "-v" "--processes" "1"))))))) (propagated-inputs - `(("htslib" ,htslib))) ; Included from installed header files. + `(("htslib" ,htslib-1.9))) ; Included from installed header files. (inputs `(("ncurses" ,ncurses) ("curl" ,curl) @@ -1963,7 +1985,7 @@ multiple sequence alignments.") (native-inputs `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. - ("samtools" ,samtools) + ("samtools" ,samtools-1.9) ("bcftools" ,bcftools) ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") -- cgit v1.2.3 From 37ba374a536453078a5ba9e81815902b256884c0 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 13 Nov 2020 16:16:43 +0100 Subject: gnu: Fix build for python-pysam. * gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9, samtools-1.9, and bcftools-1.9. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22da6ac3ff..15230a8ef2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1986,7 +1986,7 @@ multiple sequence alignments.") `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. ("samtools" ,samtools-1.9) - ("bcftools" ,bcftools) + ("bcftools" ,bcftools-1.9) ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") -- cgit v1.2.3 From e1fa3ea9fe8d01dd124c5e304bde9243876378ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Nov 2020 23:27:31 +0100 Subject: gnu: methyldackel: Update to 0.5.1. * gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1. [arguments]: Link with libbigwig. [inputs]: Add curl and libbigwig; replace htslib with htslib-1.9. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 15230a8ef2..91fcb28451 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15437,7 +15437,7 @@ patterns.") (define-public methyldackel (package (name "methyldackel") - (version "0.4.0") + (version "0.5.1") (source (origin (method git-fetch) (uri (git-reference @@ -15446,7 +15446,7 @@ patterns.") (file-name (git-file-name name version)) (sha256 (base32 - "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g")))) + "1sfhf2ap75qxpnmy1ifgmxqs18rq8mah9mcgkby73vc6h0sw99ws")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -15459,11 +15459,14 @@ patterns.") (replace 'configure (lambda* (#:key outputs #:allow-other-keys) (substitute* "Makefile" + (("-lhts ") "-lhts -lBigWig ") (("install MethylDackel \\$\\(prefix\\)" match) (string-append "install -d $(prefix); " match))) #t))))) (inputs - `(("htslib" ,htslib) + `(("curl" ,curl) ; XXX: needed by libbigwig + ("htslib" ,htslib-1.9) + ("libbigwig" ,libbigwig) ("zlib" ,zlib))) ;; Needed for tests (native-inputs -- cgit v1.2.3 From 7face25953740732c638b67294220ac779db71f4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 23 Nov 2020 10:58:29 +0200 Subject: gnu: Add python-schema-salad. * gnu/packages/bioinformatics.scm (python-schema-salad): New variable. --- gnu/packages/bioinformatics.scm | 41 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 91fcb28451..7290876450 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft -;;; Copyright © 2015, 2016 Pjotr Prins +;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2020 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner @@ -18,6 +18,7 @@ ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 Pierre Langlois +;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; ;;; This file is part of GNU Guix. ;;; @@ -112,10 +113,12 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) @@ -2579,6 +2582,42 @@ accessing bigWig files.") (define-public python2-pybigwig (package-with-python2 python-pybigwig)) +(define-public python-schema-salad + (package + (name "python-schema-salad") + (version "7.0.20200811075006") + (source + (origin + (method url-fetch) + (uri (pypi-uri "schema-salad" version)) + (sha256 + (base32 + "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg")))) + (build-system python-build-system) + (propagated-inputs + `(("python-cachecontrol" ,python-cachecontrol-0.11) + ("python-lockfile" ,python-lockfile) + ("python-mistune" ,python-mistune) + ("python-rdflib" ,python-rdflib) + ("python-rdflib-jsonld" ,python-rdflib-jsonld) + ("python-requests" ,python-requests) + ("python-ruamel.yaml" ,python-ruamel.yaml) + ("python-typing-extensions" ,python-typing-extensions))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://github.com/common-workflow-language/schema_salad") + (synopsis "Schema Annotations for Linked Avro Data (SALAD)") + (description + "Salad is a schema language for describing JSON or YAML structured linked +data documents. Salad schema describes rules for preprocessing, structural +validation, and hyperlink checking for documents described by a Salad schema. +Salad supports rich data modeling with inheritance, template specialization, +object identifiers, object references, documentation generation, code +generation, and transformation to RDF. Salad provides a bridge between document +and record oriented data modeling and the Semantic Web.") + (license license:asl2.0))) + (define-public python-dendropy (package (name "python-dendropy") -- cgit v1.2.3 From 964bc9e5fe60f19475306bf48e1813c0a79c2a88 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 23 Nov 2020 15:14:01 +0200 Subject: gnu: Add cwltool. * gnu/packages/bioinformatics.scm (cwltool): New variable. --- gnu/packages/bioinformatics.scm | 91 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 91 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7290876450..939dc79d15 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -103,6 +103,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) + #:use-module (gnu packages node) #:use-module (gnu packages ocaml) #:use-module (gnu packages pcre) #:use-module (gnu packages parallel) @@ -2618,6 +2619,96 @@ generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.") (license license:asl2.0))) +(define-public cwltool + (package + (name "cwltool") + (version "3.0.20201121085451") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/common-workflow-language/cwltool") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'loosen-version-restrictions + (lambda _ + (substitute* "setup.py" + (("== 1.5.1") ">=1.5.1") ; prov + ((", < 3.5") "")) ; shellescape + #t)) + (add-after 'unpack 'dont-use-git + (lambda _ + (substitute* "gittaggers.py" + (("self.git_timestamp_tag\\(\\)") + (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(" + (string-drop ,version 4) ")))"))) + #t)) + (add-after 'unpack 'modify-tests + (lambda _ + ;; Tries to connect to the internet. + (delete-file "tests/test_udocker.py") + (delete-file "tests/test_http_input.py") + (substitute* "tests/test_load_tool.py" + (("def test_load_graph_fragment_from_packed") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_load_graph_fragment_from_packed"))) + (substitute* "tests/test_examples.py" + (("def test_env_filtering") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_env_filtering"))) + ;; Tries to use cwl-runners. + (substitute* "tests/test_examples.py" + (("def test_v1_0_arg_empty_prefix_separate_false") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_v1_0_arg_empty_prefix_separate_false"))) + #t))))) + (propagated-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-bagit" ,python-bagit) + ("python-coloredlogs" ,python-coloredlogs) + ("python-mypy-extensions" ,python-mypy-extensions) + ("python-prov" ,python-prov) + ("python-pydot" ,python-pydot) + ("python-psutil" ,python-psutil) + ("python-rdflib" ,python-rdflib) + ("python-requests" ,python-requests) + ("python-ruamel.yaml" ,python-ruamel.yaml) + ("python-schema-salad" ,python-schema-salad) + ("python-shellescape" ,python-shellescape) + ("python-typing-extensions" ,python-typing-extensions) + ;; Not listed as needed but still necessary: + ("node" ,node))) + (native-inputs + `(("python-arcp" ,python-arcp) + ("python-humanfriendly" ,python-humanfriendly) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-mock" ,python-pytest-mock) + ("python-pytest-runner" ,python-pytest-runner) + ("python-rdflib-jsonld" ,python-rdflib-jsonld))) + (home-page + "https://github.com/common-workflow-language/common-workflow-language") + (synopsis "Common Workflow Language reference implementation") + (description + "This is the reference implementation of the @acronym{CWL, Common Workflow +Language} standards. The CWL open standards are for describing analysis +workflows and tools in a way that makes them portable and scalable across a +variety of software and hardware environments, from workstations to cluster, +cloud, and high performance computing (HPC) environments. CWL is designed to +meet the needs of data-intensive science, such as Bioinformatics, Medical +Imaging, Astronomy, Physics, and Chemistry. The @acronym{cwltool, CWL reference +implementation} is intended to be feature complete and to provide comprehensive +validation of CWL files as well as provide other tools related to working with +CWL descriptions.") + (license license:asl2.0))) + (define-public python-dendropy (package (name "python-dendropy") -- cgit v1.2.3 From e7e73f750fa276c66995f3b9967dd2639be19cf8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 23 Nov 2020 11:42:37 -0500 Subject: gnu: imp: Migrate to Python 3. * gnu/packages/bioinformatics.scm (imp) [arguments]: Enable tests by removing the #:tests? argument. Specify the arguments to pass to the ctest test running via the #:configure-flags argument. [inputs]: Add cgal and opencv. Remove python-2. Move swig to... [native-inputs]: ...here. Add python-wrapper. [propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas, python2-scikit-learn and python2-networkx by python-numpy, python-scipy, python-pandas, python-scikit-learn and python-networkx, respectively. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++---------- 1 file changed, 35 insertions(+), 11 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 939dc79d15..bd5a32a9b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu -;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2019, 2020 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling @@ -66,6 +66,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages code) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages cran) @@ -82,6 +83,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) @@ -91,6 +93,7 @@ #:use-module (gnu packages haskell-web) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) + #:use-module (gnu packages image-processing) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) @@ -11169,23 +11172,44 @@ programs for inferring phylogenies (evolutionary trees).") "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj")))) (build-system cmake-build-system) (arguments - `(;; FIXME: Some tests fail because they produce warnings, others fail - ;; because the PYTHONPATH does not include the modeller's directory. - #:tests? #f)) + `( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used + ;; below to have an effect. + #:cmake ,cmake + #:configure-flags + (let ((disabled-tests + '("expensive" ;exclude expensive tests + "IMP.modeller" ;fail to import its own modules + "IMP.parallel-test_sge.py" ;fail in build container + ;; The following test fails non-reproducibly on + ;; an inexact numbers assertion. + "IMP.em-medium_test_local_fitting.py"))) + (list + (string-append + "-DCMAKE_CTEST_ARGUMENTS=" + (string-join + (list "-L" "-tests?-" ;select only tests + "-E" (format #f "'(~a)'" (string-join disabled-tests "|"))) + ";")))))) + (native-inputs + `(("python" ,python-wrapper) + ("swig" ,swig))) (inputs `(("boost" ,boost) + ("cgal" ,cgal) ("gsl" ,gsl) - ("swig" ,swig) ("hdf5" ,hdf5) ("fftw" ,fftw) ("eigen" ,eigen) - ("python" ,python-2))) + ;; Enabling MPI causes the build to use all the available memory and + ;; fail (tested on a machine with 32 GiB of RAM). + ;;("mpi" ,openmpi) + ("opencv" ,opencv))) (propagated-inputs - `(("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-pandas" ,python2-pandas) - ("python2-scikit-learn" ,python2-scikit-learn) - ("python2-networkx" ,python2-networkx))) + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-pandas" ,python-pandas) + ("python-scikit-learn" ,python-scikit-learn) + ("python-networkx" ,python-networkx))) (home-page "https://integrativemodeling.org") (synopsis "Integrative modeling platform") (description "IMP's broad goal is to contribute to a comprehensive -- cgit v1.2.3 From 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 24 Nov 2020 02:15:16 -0500 Subject: gnu: tadbit: Update to 1.0.1. * gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1. [arguments]: Remove #:tests? and #:python arguments. [phases]{fix-problems-with-setup.py}: Remove no longer needed steps. {check}: Override phase. [native-inputs]: Add glib and pkg-config. [inputs]: Add python-future and python-h5py. --- gnu/packages/bioinformatics.scm | 33 ++++++++++++++++++--------------- 1 file changed, 18 insertions(+), 15 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bd5a32a9b7..b3b4d1e1c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -66,6 +66,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages code) + #:use-module (gnu packages commencement) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) @@ -11227,7 +11228,7 @@ applications for tackling some common problems in a user-friendly way.") (define-public tadbit (package (name "tadbit") - (version "0.2.0") + (version "1.0.1") (source (origin (method git-fetch) (uri (git-reference @@ -11236,21 +11237,13 @@ applications for tackling some common problems in a user-friendly way.") (file-name (git-file-name name version)) (sha256 (base32 - "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0")))) + "0hqrlymh2a2bimcfdvlssy1x5h1lp3h1c5a7jj11hmcqczzqn3ni")))) (build-system python-build-system) (arguments - `(;; Tests are included and must be run after installation, but - ;; they are incomplete and thus cannot be run. - #:tests? #f - #:python ,python-2 - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-problems-with-setup.py (lambda* (#:key outputs #:allow-other-keys) - ;; setup.py opens these files for writing - (chmod "_pytadbit/_version.py" #o664) - (chmod "README.rst" #o664) - ;; Don't attempt to install the bash completions to ;; the home directory. (rename-file "extras/.bash_completion" @@ -11262,15 +11255,25 @@ applications for tackling some common problems in a user-friendly way.") "/etc/bash_completion.d\"")) (("extras/\\.bash_completion") "extras/tadbit")) + #t)) + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "python3" "test/test_all.py") #t))))) + (native-inputs + `(("glib" ,glib "bin") ;for gtester + ("pkg-config" ,pkg-config))) (inputs ;; TODO: add Chimera for visualization `(("imp" ,imp) ("mcl" ,mcl) - ("python2-scipy" ,python2-scipy) - ("python2-numpy" ,python2-numpy) - ("python2-matplotlib" ,python2-matplotlib) - ("python2-pysam" ,python2-pysam))) + ("python-future" ,python-future) + ("python-h5py" ,python-h5py) + ("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-matplotlib" ,python-matplotlib) + ("python-pysam" ,python-pysam))) (home-page "https://3dgenomes.github.io/TADbit/") (synopsis "Analyze, model, and explore 3C-based data") (description -- cgit v1.2.3