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authorLev Levitsky2019-09-24 19:38:10 +0300
committerLev Levitsky2019-09-24 19:38:10 +0300
commitcae765a824ac3ca8cfa75d2e50dd2afc32be67e9 (patch)
tree53712f8337912f0148b7a2b487b4cfe2a4c1fb0e
parent5904e2ea902ed1195ee8752c43e9b759d40eaa0b (diff)
downloadaur-cae765a824ac3ca8cfa75d2e50dd2afc32be67e9.tar.gz
Fix for version 3.04
-rw-r--r--.SRCINFO4
-rw-r--r--PKGBUILD17
-rw-r--r--percolator.patch24
3 files changed, 8 insertions, 37 deletions
diff --git a/.SRCINFO b/.SRCINFO
index e1a333ceff9..84a2e2d3511 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
pkgbase = percolator-git
pkgdesc = Software for postprocessing of shotgun proteomics data + format converters + Elude tool
- pkgver = 3.02.01.r8.gf97ae1d
+ pkgver = 3.04
pkgrel = 1
url = http://percolator.ms/
arch = x86_64
@@ -14,9 +14,7 @@ pkgbase = percolator-git
depends = libtirpc-compat
depends = boost
source = source::git+https://github.com/percolator/percolator
- source = percolator.patch
md5sums = SKIP
- md5sums = 53c592a9db82da8474907a617ea688fb
pkgname = percolator-git
pkgdesc = Percolator and qvality, two post processors for shotgun proteomics data.
diff --git a/PKGBUILD b/PKGBUILD
index 3c8cc0515bc..00c595e5b90 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,7 +1,7 @@
# Maintainer: Lev Levitsky <levlev@mail.ru>
pkgbase="percolator-git"
pkgname=('percolator-git' 'percolator-converters-git' 'elude-git')
-pkgver=3.02.01.r8.gf97ae1d
+pkgver=3.04
pkgrel=1
pkgdesc="Software for postprocessing of shotgun proteomics data + format converters + Elude tool"
url="http://percolator.ms/"
@@ -9,10 +9,8 @@ license=('Apache')
depends=('xerces-c' 'sqlite' 'libtirpc-compat' 'boost')
arch=('x86_64')
makedepends=('git' 'xsd' 'cmake' 'zlib')
-source=('source::git+https://github.com/percolator/percolator'
- 'percolator.patch')
-md5sums=('SKIP'
- '53c592a9db82da8474907a617ea688fb')
+source=('source::git+https://github.com/percolator/percolator')
+md5sums=('SKIP')
pkgver() {
cd "${srcdir}/source"
@@ -21,7 +19,6 @@ pkgver() {
prepare() {
cd "${srcdir}/source"
- patch -p1 -i "$srcdir/${pkgname%-git}.patch"
cd "$BUILDDIR"
for d in "${pkgname[@]}"; do
mkdir "${d%-git}"
@@ -36,10 +33,10 @@ build() {
echo "------------------------"
echo "Running cmake for percolator ..."
echo "................................"
- cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=ON "${srcdir}/source"
+ cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=ON -DCMAKE_PREFIX_PATH="/usr/include;/usr/lib" -DCMAKE_CXX_FLAGS="-l tirpc" "${srcdir}/source"
echo "Running make for percolator ..."
echo "..............................."
- make
+ make -j 4
echo "------------------------"
echo "Building converters ..."
echo "------------------------"
@@ -49,7 +46,7 @@ build() {
cmake -DTARGET_ARCH=x86_64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/converters"
echo "Running make for percolator-converters ..."
echo ".........................................."
- make
+ make -j 4
echo "------------------------"
echo "Building Elude ..."
echo "------------------------"
@@ -59,7 +56,7 @@ build() {
cmake -DTARGET_ARCH=x86_64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/elude_tool"
echo "Running make for elude ..."
echo ".........................."
- make
+ make -j 4
}
package_percolator-git() {
diff --git a/percolator.patch b/percolator.patch
deleted file mode 100644
index 22fdc38b4a8..00000000000
--- a/percolator.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-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
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 09aa167..80f6105 100755
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -161,4 +161,5 @@ ENDIF(CRUX)
- ###############################################################################
-
- add_subdirectory(qvality)
--
-+include_directories(/usr/include/rpc)
-+target_link_libraries(percolator tirpc)