From 241e122193e6eee900cab1f3a1caec2f90603560 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 29 Jan 2015 10:35:52 +0100 Subject: gnu: bowtie: fix build errors * gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and add Makefile patch. * gnu/packages/patches/bowtie-fix-makefile.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. --- gnu/packages/bioinformatics.scm | 6 +++-- gnu/packages/patches/bowtie-fix-makefile.patch | 31 ++++++++++++++++++++++++++ 2 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/bowtie-fix-makefile.patch (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6c3379af..620c8090b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014 Ricardo Wurmus +;;; Copyright © 2014, 2015 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -95,7 +95,8 @@ BED, GFF/GTF, VCF.") (("^CPP = .*$") "CPP = g++") ;; replace BUILD_HOST and BUILD_TIME for deterministic build (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") - (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))) + (patches (list (search-patch "bowtie-fix-makefile.patch"))))) (build-system gnu-build-system) (inputs `(("perl" ,perl) ("perl-clone" ,perl-clone) @@ -133,6 +134,7 @@ aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.") + (supported-systems '("x86_64-linux")) (license license:gpl3+))) (define-public samtools diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/packages/patches/bowtie-fix-makefile.patch new file mode 100644 index 0000000000..5ac65731cb --- /dev/null +++ b/gnu/packages/patches/bowtie-fix-makefile.patch @@ -0,0 +1,31 @@ +From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001 +From: Valentin Antonescu +Date: Tue, 2 Dec 2014 11:19:13 -0500 +Subject: [PATCH] Make sure the Mavericks test happens only under Darwin. + +--- + Makefile | 11 +++++------ + 1 file changed, 5 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index d74f7c8..a4cdfa7 100644 +--- a/Makefile ++++ b/Makefile +@@ -54,12 +54,11 @@ endif + MACOS = 0 + ifneq (,$(findstring Darwin,$(shell uname))) + MACOS = 1 +-endif +- +-ifneq (,$(findstring 13,$(shell uname -r))) +- CPP = clang++ +- CC = clang +- EXTRA_FLAGS += -stdlib=libstdc++ ++ ifneq (,$(findstring 13,$(shell uname -r))) ++ CPP = clang++ ++ CC = clang ++ EXTRA_FLAGS += -stdlib=libstdc++ ++ endif + endif + + POPCNT_CAPABILITY ?= 1 -- cgit 1.4.1