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 @@ (define-public macs ;; 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 @@ (define-public macs `(("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 @@ (define-public macs (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 @@ (define-public macs (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 @@ (define-public macs (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