forked from sjackman/linuxbrew-core
-
Notifications
You must be signed in to change notification settings - Fork 0
/
abyss.rb
58 lines (50 loc) · 2.23 KB
/
abyss.rb
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
class Abyss < Formula
desc "Genome sequence assembler for short reads"
homepage "https://www.bcgsc.ca/resources/gsc-software-centre"
url "https://github.com/bcgsc/abyss/releases/download/2.2.3/abyss-2.2.3.tar.gz"
sha256 "ac7679ececbdd89cc050998eae31fa5f8bf7cdab6a0c05eb5eb1e3867c7e75cb"
bottle do
cellar :any
sha256 "fe5e65727d390f31e0e847e30da9a6b931c7b1b5f3c0a4e6459b5aa0f4eb0ad9" => :catalina
sha256 "d982f22bbc71a21271eb01441f4189366e91bfb3dc8c9718df09307eb89bf11e" => :mojave
sha256 "482a9754933a932ca3d8860de7f753b72a1a344ddaf40104849ba999218d86a8" => :high_sierra
sha256 "7bf03484adc48d8071eaab2ac4ed55c0cd3f6da399d28ad2f257a3aca528ea38" => :x86_64_linux
end
head do
url "https://github.com/bcgsc/abyss.git"
depends_on "autoconf" => :build
depends_on "automake" => :build
depends_on "multimarkdown" => :build
end
depends_on "boost" => :build
depends_on "google-sparsehash" => :build
depends_on "gcc" if OS.mac?
depends_on "open-mpi"
fails_with :clang # no OpenMP support
resource("testdata") do
url "https://www.bcgsc.ca/sites/default/files/bioinformatics/software/abyss/releases/1.3.4/test-data.tar.gz"
sha256 "28f8592203daf2d7c3b90887f9344ea54fda39451464a306ef0226224e5f4f0e"
end
def install
ENV.delete("HOMEBREW_SDKROOT") if MacOS.version >= :mojave && MacOS::CLT.installed?
system "./autogen.sh" if build.head?
system "./configure", "--enable-maxk=128",
"--prefix=#{prefix}",
"--with-boost=#{Formula["boost"].include}",
"--with-mpi=#{Formula["open-mpi"].prefix}",
"--with-sparsehash=#{Formula["google-sparsehash"].prefix}",
"--disable-dependency-tracking",
"--disable-silent-rules"
system "make", "install"
end
test do
testpath.install resource("testdata")
if OS.mac? || which("column")
system "#{bin}/abyss-pe", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
else
# Fix error: abyss-tabtomd: column: not found
system "#{bin}/abyss-pe", "unitigs", "scaffolds", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
end
system "#{bin}/abyss-fac", "ts-unitigs.fa"
end
end