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authorLev Levitsky2015-07-30 05:38:45 +0300
committerLev Levitsky2015-07-30 05:38:45 +0300
commit78a714307ff2e796eb8da4a2552d22703b943795 (patch)
tree707224994d848a2f25f6d82f46901e7eb283cc34
downloadaur-78a714307ff2e796eb8da4a2552d22703b943795.tar.gz
Initial commit
-rw-r--r--.SRCINFO25
-rw-r--r--PKGBUILD64
-rw-r--r--percolator.patch13
3 files changed, 102 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 00000000000..9ff5209d5fb
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,25 @@
+pkgbase = percolator-git
+ pkgdesc = Software for postprocessing of shotgun proteomics data + format converters + Elude tool
+ pkgver = 2.10.r1.gd92d600
+ pkgrel = 1
+ url = http://per-colator.com/
+ arch = x86_64
+ arch = i686
+ license = Apache
+ makedepends = git
+ makedepends = xsd
+ makedepends = cmake
+ makedepends = boost
+ makedepends = zlib
+ depends = tokyocabinet
+ depends = xerces-c
+ depends = sqlite
+ provides = percolator
+ conflicts = percolator
+ source = source::git+https://github.com/percolator/percolator
+ source = percolator.patch
+ md5sums = SKIP
+ md5sums = 4e1432640f09fa3dc2f3d9894ec380f4
+
+pkgname = percolator-git
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 00000000000..a5d5bc8eb64
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,64 @@
+# Maintainer: Lev Levitsky <levlev@mail.ru>
+pkgname=percolator-git
+pkgver=2.10.r1.gd92d600
+pkgrel=1
+pkgdesc="Software for postprocessing of shotgun proteomics data + format converters + Elude tool"
+url="http://per-colator.com/"
+license=('Apache')
+depends=('tokyocabinet' 'xerces-c' 'sqlite')
+arch=('x86_64' 'i686')
+makedepends=('git' 'xsd' 'cmake' 'boost' 'zlib' )
+provides=("${pkgname%-git}")
+conflicts=("${pkgname%-git}")
+source=('source::git+https://github.com/percolator/percolator'
+ 'percolator.patch')
+md5sums=('SKIP'
+ '4e1432640f09fa3dc2f3d9894ec380f4')
+
+pkgver() {
+ cd "${srcdir}/source"
+ git describe --match='rel*' --tags | sed 's/\([^-]*-g\)/r\1/;s/rel-//;s/-/./g'
+}
+
+prepare() {
+ cd "${srcdir}/source"
+ patch -p1 -i "$srcdir/${pkgname%-git}.patch"
+}
+
+build() {
+ cd "$BUILDDIR"
+ mkdir percolator converters elude
+ cd percolator
+ echo "------------------------"
+ echo "Building percolator ..."
+ echo "------------------------"
+ cmake "${srcdir}/source"
+ make
+ echo "------------------------"
+ echo "Building converters ..."
+ echo "------------------------"
+ cd ../converters
+ cmake -DSERIALIZE="TokyoCabinet" "${srcdir}/source/src/converters"
+ make
+ echo "------------------------"
+ echo "Building Elude ..."
+ echo "------------------------"
+ cd ../elude
+ cmake "${srcdir}/source/src/elude_tool"
+ make
+}
+
+package() {
+ cd "$BUILDDIR/percolator"
+ make DESTDIR="$pkgdir/" install
+ cd "$BUILDDIR/converters"
+ make DESTDIR="$pkgdir/" install
+ cd "$BUILDDIR/elude"
+ make DESTDIR="$pkgdir/" install
+ install -D "${srcdir}/source/license.txt" "${pkgdir}/usr/share/licenses/percolator/license.txt"
+ install -d "$pkgdir/usr/bin"
+ install -d "$pkgdir/usr/share/${pkgname%-git}"
+ mv "$pkgdir"/usr/local/share/* "$pkgdir/usr/share/${pkgname%-git}"
+ mv "$pkgdir"/usr/local/bin/* "$pkgdir/usr/bin"
+ rm -r "$pkgdir/usr/local"
+}
diff --git a/percolator.patch b/percolator.patch
new file mode 100644
index 00000000000..add4b7ca1ac
--- /dev/null
+++ b/percolator.patch
@@ -0,0 +1,13 @@
+diff --git a/cmake/FindXsd.cmake b/cmake/FindXsd.cmake
+index 5b4e084..d11970b 100755
+--- a/cmake/FindXsd.cmake
++++ b/cmake/FindXsd.cmake
+@@ -20,7 +20,7 @@ PATH_SUFFIXES
+
+ FIND_PROGRAM(XSD_EXECUTABLE
+ NAMES
+- xsd xsdcxx
++ xsdcxx xsd
+ PATHS
+ $ENV{XSDDIR}/bin
+ /usr/local/bin