diff options
author | apolih | 2016-07-16 15:58:17 -0500 |
---|---|---|
committer | apolih | 2016-07-16 15:58:17 -0500 |
commit | e4181a512dd73a4285da93de7e2a582bb1d148cf (patch) | |
tree | c74ef177684c6e49ddab795d1f5e03173240345a | |
parent | 3c7492d6cb18a11913d17d52655e0d6c09694abb (diff) | |
download | aur-e4181a512dd73a4285da93de7e2a582bb1d148cf.tar.gz |
update pkgver
-rw-r--r-- | .SRCINFO | 8 | ||||
-rw-r--r-- | PKGBUILD | 4 | ||||
-rw-r--r-- | ngs.patch | 46 |
3 files changed, 16 insertions, 42 deletions
@@ -1,6 +1,6 @@ pkgbase = ngs pkgdesc = A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. - pkgver = 1.2.4 + pkgver = 1.2.5 pkgrel = 1 url = https://github.com/ncbi/ngs arch = x86_64 @@ -9,10 +9,10 @@ pkgbase = ngs depends = perl-file-copy-recursive depends = zlib provides = ngs - source = https://github.com/ncbi/ngs/archive/1.2.4.tar.gz + source = https://github.com/ncbi/ngs/archive/1.2.5.tar.gz source = ngs.patch - sha256sums = 6c7a2a2e3659c46a511f9c16f29fde413b388aa0dc5b15324dc631bddd49ee86 - sha256sums = e40cb6963e3dc07fcd66ed35730193c6f1a448d8a446d243038f7ebbd62f739f + sha256sums = 2a32c30d1611f8ce68aba81e5b44369969c6d32bcebc37aa41be2cdbaa76c113 + sha256sums = 004eb006e9bbd9f4368c54663e7d991833aeae3e9c6583e61566340cd04d5bb6 pkgname = ngs @@ -2,7 +2,7 @@ # Maintainer: Aaron Baker <aa{last name}99{at}gmail{dt}org> pkgname=ngs -pkgver=1.2.4 +pkgver=1.2.5 pkgrel=1 pkgdesc="A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing." arch=('x86_64') @@ -11,7 +11,7 @@ depends=('java-environment' 'perl-file-copy-recursive' 'zlib') provides=('ngs') license=('custom:PublicDomain') source=("https://github.com/ncbi/ngs/archive/$pkgver.tar.gz" "$pkgname.patch") -sha256sums=('6c7a2a2e3659c46a511f9c16f29fde413b388aa0dc5b15324dc631bddd49ee86' 'e40cb6963e3dc07fcd66ed35730193c6f1a448d8a446d243038f7ebbd62f739f') +sha256sums=('2a32c30d1611f8ce68aba81e5b44369969c6d32bcebc37aa41be2cdbaa76c113' '004eb006e9bbd9f4368c54663e7d991833aeae3e9c6583e61566340cd04d5bb6') prepare(){ cd "${pkgname}-${pkgver}" diff --git a/ngs.patch b/ngs.patch index cbba1b066b55..27bcb5497b44 100644 --- a/ngs.patch +++ b/ngs.patch @@ -1,32 +1,6 @@ -diff -aur ngs-1.2.3.pristine/Makefile ngs-1.2.3.new/Makefile ---- ngs-1.2.3.pristine/Makefile 2015-11-23 18:38:45.000000000 +0000 -+++ ngs-1.2.3.new/Makefile 2016-01-25 21:42:41.455818616 +0000 -@@ -29,7 +29,6 @@ - SUBDIRS = \ - ngs-sdk \ - ngs-java \ -- ngs-python \ - - - SUBDIRS_CLN = \ -diff -aur ngs-1.2.3.pristine/ngs-bam/setup/install.perl ngs-1.2.3.new/ngs-bam/setup/install.perl ---- ngs-1.2.3.pristine/ngs-bam/setup/install.perl 2015-11-23 18:38:45.000000000 +0000 -+++ ngs-1.2.3.new/ngs-bam/setup/install.perl 2016-01-25 22:20:30.522404231 +0000 -@@ -81,11 +81,9 @@ - prepare(); - - my $LINUX_ROOT; --++$LINUX_ROOT if (linux_root()); - my $ROOT = ''; - if ($OPT{root}) { - $ROOT = "$OPT{root}/root"; -- ++$LINUX_ROOT; - foreach ("$ROOT/usr/include", "$ROOT/etc/profile.d") { - unless (-e $_) { - print "mkdir -p $_... "; -diff -aur ngs-1.2.3.pristine/ngs-java/Makefile.java ngs-1.2.3.new/ngs-java/Makefile.java ---- ngs-1.2.3.pristine/ngs-java/Makefile.java 2015-11-23 18:38:45.000000000 +0000 -+++ ngs-1.2.3.new/ngs-java/Makefile.java 2016-01-25 21:16:43.505874267 +0000 +diff -aur ngs-1.2.5.pristine/ngs-java/Makefile.java ngs-1.2.5.new/ngs-java/Makefile.java +--- ngs-1.2.5.pristine/ngs-java/Makefile.java 2016-07-15 18:45:56.228525816 +0000 ++++ ngs-1.2.5.new/ngs-java/Makefile.java 2016-07-15 18:46:43.595193491 +0000 @@ -59,12 +59,13 @@ JAR_TARGET = $(INST_JARDIR)/ngs-java.jar DOC_TARGET = $(INST_SHAREDIR)/doc/ @@ -47,9 +21,9 @@ diff -aur ngs-1.2.3.pristine/ngs-java/Makefile.java ngs-1.2.3.new/ngs-java/Makef install: $(TARGETS) $(INST_JARDIR) $(INST_JARDIR)/ngs-java.jar.$(VERSION) copydocs copyexamples ifeq (true, $(LINUX_ROOT)) -diff -aur ngs-1.2.3.pristine/ngs-python/Makefile.python ngs-1.2.3.new/ngs-python/Makefile.python ---- ngs-1.2.3.pristine/ngs-python/Makefile.python 2015-11-23 18:38:45.000000000 +0000 -+++ ngs-1.2.3.new/ngs-python/Makefile.python 2016-01-25 21:19:48.709200984 +0000 +diff -aur ngs-1.2.5.pristine/ngs-python/Makefile.python ngs-1.2.5.new/ngs-python/Makefile.python +--- ngs-1.2.5.pristine/ngs-python/Makefile.python 2016-07-15 18:45:56.235192482 +0000 ++++ ngs-1.2.5.new/ngs-python/Makefile.python 2016-07-15 18:47:44.511861457 +0000 @@ -56,7 +56,7 @@ install: $(TARGETS) $(INST_PYTHONDIR) copyexamples ifeq (0, $(shell id -u)) @@ -68,9 +42,9 @@ diff -aur ngs-1.2.3.pristine/ngs-python/Makefile.python ngs-1.2.3.new/ngs-python else @ echo "Installing ngs package..." -diff -aur ngs-1.2.3.pristine/ngs-sdk/Makefile.install ngs-1.2.3.new/ngs-sdk/Makefile.install ---- ngs-1.2.3.pristine/ngs-sdk/Makefile.install 2015-11-23 18:38:45.000000000 +0000 -+++ ngs-1.2.3.new/ngs-sdk/Makefile.install 2016-01-25 21:09:31.642556359 +0000 +diff -aur ngs-1.2.5.pristine/ngs-sdk/Makefile.install ngs-1.2.5.new/ngs-sdk/Makefile.install +--- ngs-1.2.5.pristine/ngs-sdk/Makefile.install 2016-07-15 18:45:56.248525816 +0000 ++++ ngs-1.2.5.new/ngs-sdk/Makefile.install 2016-07-15 18:48:18.855195523 +0000 @@ -63,11 +63,12 @@ INCLUDE_SYMLINK = $(ROOT)/usr/include/ngs PROFILE_FILE = $(ROOT)/etc/profile.d/ngs-sdk @@ -80,12 +54,12 @@ diff -aur ngs-1.2.3.pristine/ngs-sdk/Makefile.install ngs-1.2.3.new/ngs-sdk/Make - LINUX_ROOT = true - endif -endif -+LINUX_ROOT = false +#ifeq (linux, $(OS)) +# ifeq (0, $(shell id -u)) +# LINUX_ROOT = true +# endif +#endif ++LINUX_ROOT = false install: copylibs copyincludes copyexamples ifeq (true, $(LINUX_ROOT)) |