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authorLev Levitsky2019-02-19 22:24:49 +0300
committerLev Levitsky2019-02-19 22:24:49 +0300
commit5904e2ea902ed1195ee8752c43e9b759d40eaa0b (patch)
tree24faa1f96f4445f4e7cc3d14f1534fdb7b291416
parent1844e351feb5d32a96b3b71a34eb09ff1b35c4c6 (diff)
downloadaur-5904e2ea902ed1195ee8752c43e9b759d40eaa0b.tar.gz
Update patch and dependencies
-rw-r--r--.SRCINFO7
-rw-r--r--PKGBUILD26
-rw-r--r--percolator.patch11
3 files changed, 34 insertions, 10 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 5be63f55cf7..e1a333ceff9 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
+ pkgver = 3.02.01.r8.gf97ae1d
pkgrel = 1
url = http://percolator.ms/
arch = x86_64
@@ -8,14 +8,15 @@ pkgbase = percolator-git
makedepends = git
makedepends = xsd
makedepends = cmake
- makedepends = boost
makedepends = zlib
depends = xerces-c
depends = sqlite
+ depends = libtirpc-compat
+ depends = boost
source = source::git+https://github.com/percolator/percolator
source = percolator.patch
md5sums = SKIP
- md5sums = 4e1432640f09fa3dc2f3d9894ec380f4
+ md5sums = 53c592a9db82da8474907a617ea688fb
pkgname = percolator-git
pkgdesc = Percolator and qvality, two post processors for shotgun proteomics data.
diff --git a/PKGBUILD b/PKGBUILD
index c3fefe2ba64..3c8cc0515bc 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,18 +1,18 @@
# Maintainer: Lev Levitsky <levlev@mail.ru>
pkgbase="percolator-git"
pkgname=('percolator-git' 'percolator-converters-git' 'elude-git')
-pkgver=3.02
+pkgver=3.02.01.r8.gf97ae1d
pkgrel=1
pkgdesc="Software for postprocessing of shotgun proteomics data + format converters + Elude tool"
url="http://percolator.ms/"
license=('Apache')
-depends=('xerces-c' 'sqlite')
+depends=('xerces-c' 'sqlite' 'libtirpc-compat' 'boost')
arch=('x86_64')
-makedepends=('git' 'xsd' 'cmake' 'boost' 'zlib')
+makedepends=('git' 'xsd' 'cmake' 'zlib')
source=('source::git+https://github.com/percolator/percolator'
'percolator.patch')
md5sums=('SKIP'
- '4e1432640f09fa3dc2f3d9894ec380f4')
+ '53c592a9db82da8474907a617ea688fb')
pkgver() {
cd "${srcdir}/source"
@@ -34,19 +34,31 @@ build() {
echo "------------------------"
echo "Building percolator ..."
echo "------------------------"
- cmake -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=ON "${srcdir}/source"
+ echo "Running cmake for percolator ..."
+ echo "................................"
+ cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=ON "${srcdir}/source"
+ echo "Running make for percolator ..."
+ echo "..............................."
make
echo "------------------------"
echo "Building converters ..."
echo "------------------------"
cd "../${pkgname[1]%-git}"
- cmake -DTARGET_ARCH=amd64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/converters"
+ echo "Running cmake for percolator-converters ..."
+ echo "..........................................."
+ cmake -DTARGET_ARCH=x86_64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/converters"
+ echo "Running make for percolator-converters ..."
+ echo ".........................................."
make
echo "------------------------"
echo "Building Elude ..."
echo "------------------------"
cd "../${pkgname[2]%-git}"
- cmake -DTARGET_ARCH=amd64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/elude_tool"
+ echo "Running cmake for elude ..."
+ echo "..........................."
+ 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
}
diff --git a/percolator.patch b/percolator.patch
index add4b7ca1ac..22fdc38b4a8 100644
--- a/percolator.patch
+++ b/percolator.patch
@@ -11,3 +11,14 @@ index 5b4e084..d11970b 100755
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)