blob: ade89bef795d208e61222a3c946bd947757cd393 (
plain)
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
59
60
61
62
63
64
65
66
67
68
69
|
# Maintainer: a821 < at mail dot de >
# Contributor: Grey Christoforo <first name [at] last name [dot] net>
pkgname=bowtie2-git
pkgver=2.5.4.r0.g4cf8d52
pkgrel=1
pkgdesc="Tool for aligning sequencing reads to long reference sequences"
arch=("x86_64")
url="https://bowtie-bio.sourceforge.net/bowtie2"
license=('GPL-3.0-only')
depends=('perl' 'python')
makedepends=('git' 'jdk-openjdk' 'cmake')
source=("$pkgname::git+https://github.com/BenLangmead/bowtie2"
"git+https://github.com/simd-everywhere/simde-no-tests.git"
"git+https://github.com/ch4rr0/libsais.git"
"git+https://github.com/ncbi/sra-tools.git"
"git+https://github.com/ncbi/ncbi-vdb.git"
)
conflicts=('bowtie2')
provides=('bowtie2')
sha256sums=('SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP')
pkgver() {
cd $pkgname
git describe --long --tags | sed 's/^v//;s/-/.r/;s/-/./g'
}
prepare() {
cd $pkgname
git submodule init
git config submodule.third_party/libsais.url "$srcdir/libsais"
git config submodule.third_party/simde.url "$srcdir/simde-no-tests"
git -c protocol.file.allow=always submodule update
sed -i 's#/vdb3##' Makefile # fix bug in Makefile
# get sra-tools version and prepare temp directory
local sra_ver=$(sed -n -e 's/^SRA_TOOLS_VER.*= *//p' Makefile)
local vdb_ver=$(sed -n -e 's/^VDB_VER.*= *//p' Makefile)
mkdir -p .tmp
# copy sra-tools to temp dir
cd "$srcdir/ncbi-vdb"
git worktree add ../bowtie2-git/.tmp/ncbi-vdb-$vdb_ver $vdb_ver
cd "$srcdir/sra-tools"
git worktree add ../bowtie2-git/.tmp/sra-tools-$sra_ver $sra_ver
}
build() {
cd $pkgname
make libsais USE_SAIS_OPENMP=1
make sra-deps
make PREFIX=/usr USE_SRA=1 USE_SAIS_OPENMP=1
}
package() {
cd $pkgname
make PREFIX=/usr DESTDIR="$pkgdir" install
install -Dm644 -t "$pkgdir/usr/share/doc/$pkgname" \
AUTHORS BOWTIE2_VERSION MANUAL* NEWS README.md TUTORIAL
cp -r doc example "$pkgdir/usr/share/doc/$pkgname"
}
# vim: set ts=4 sw=4 et:
|