Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ema 0.7.0 #1838

Merged
merged 1 commit into from
Aug 22, 2024
Merged

ema 0.7.0 #1838

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 20 additions & 14 deletions Formula/ema.rb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,8 @@ class Ema < Formula
desc "Fast and accurate alignment of linked reads"
homepage "https://ema.csail.mit.edu"
url "https://github.com/arshajii/ema.git",
tag: "v0.6.2", revision: "893be3470e613043bf75fefdc73396d40c3bc2bc"
tag: "v0.7.0", revision: "2e0d8a2a00b08c246a125566cd9ee636879cc457"
license "MIT"
revision 1
head "https://github.com/arshajii/ema.git"

bottle do
Expand All @@ -14,12 +13,14 @@ class Ema < Formula
sha256 cellar: :any_skip_relocation, x86_64_linux: "c6f4bfa74c1252a1f1e7b338c5ad0160bf7a384746eb9905ecb91d344b3dd483"
end

fails_with :clang # needs openmp
depends_on "pigz"
depends_on "sambamba"
depends_on "samtools"

if OS.mac?
depends_on "gcc" # needs openmp
else
depends_on "zlib"
uses_from_macos "zlib"

on_macos do
depends_on "libomp"
end

resource "4M-with-alts" do
Expand All @@ -29,13 +30,18 @@ class Ema < Formula
end

def install
# Fix error: This file requires compiler and library support for the ISO C++ 2011 standard.
# Need patch: https://github.com/lh3/bwa/issues/314
inreplace "bwa/Makefile", "-Wno-unused-function -O2", "-Wno-unused-function -O2 -fcommon"
inreplace "bwa/rle.h", "const uint8_t rle_auxtab[8];", "extern const uint8_t rle_auxtab[8];"

ENV.deparallelize
system "make"
if OS.mac?
inreplace "Makefile" do |s|
s.gsub! "-lm -lz -lpthread", "-lm -lz -lpthread -lomp"
s.gsub! "CFLAGS = -std=gnu99 -march=x86-64 -O3 -fopenmp",
"CFLAGS = -std=gnu99 -march=native -O3 -Xpreprocessor -fopenmp"
s.gsub! "LFLAGS = -lstdc++ -march=x86-64 -O3 -flto -fopenmp",
"LFLAGS = -lstdc++ -march=native -O3 -flto -Xpreprocessor -fopenmp"
s.gsub! "CPPFLAGS = -c -std=c++11 -O3 -march=x86-64 -pthread",
"CPPFLAGS = -std=c++11 -O3 -march=native -Xpreprocessor -fopenmp"
end
end
system "make", "CC=#{ENV.cc}", "CXX=#{ENV.cxx}"
bin.install "ema"
prefix.install resource("4M-with-alts")
end
Expand Down