Initial commit for ngs-python, 2.9.6

Signed-off-by: George Amanakis <gamanakis@gmail.com>

4 files changed, 169 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..38be1b48b052
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,22 @@
+pkgbase = ngs-python
+	pkgdesc = A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
+	pkgver = 2.9.6
+	pkgrel = 1
+	url = https://github.com/ncbi/ngs
+	arch = x86_64
+	license = custom:PublicDomain
+	depends = java-environment
+	depends = perl-file-copy-recursive
+	depends = zlib
+	depends = ncbi-vdb
+	depends = ngs
+	provides = ngs-python
+	source = https://github.com/ncbi/ngs/archive/2.9.6.tar.gz
+	source = ngs.patch
+	source = ngs-python.patch
+	md5sums = d87f96dcfcaf4967ddbbf8de761641f8
+	md5sums = 3973d35d7a1b252eb6a426403a652ef9
+	md5sums = 105d75eb6e144af86569e1240e959702
+
+pkgname = ngs-python
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..7432e9ef6183
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,52 @@
+# This is the PKGBUILD for ngs-python
+# Maintainer: Georgios Amanakis <g_amanakis{at}yahoo{dt}com>
+
+pkgname=ngs-python
+_pkgname=ngs
+pkgver=2.9.6
+pkgrel=1
+pkgdesc="A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing."
+arch=('x86_64')
+url="https://github.com/ncbi/ngs"
+depends=('java-environment' 'perl-file-copy-recursive' 'zlib' 'ncbi-vdb' 'ngs')
+provides=('ngs-python')
+license=('custom:PublicDomain')
+source=("https://github.com/ncbi/ngs/archive/$pkgver.tar.gz" "ngs.patch" "ngs-python.patch")
+md5sums=('d87f96dcfcaf4967ddbbf8de761641f8'
+         '3973d35d7a1b252eb6a426403a652ef9'
+         '105d75eb6e144af86569e1240e959702')
+
+prepare(){
+  cd "${_pkgname}-${pkgver}"
+  # ncbi build process frequently checks if we are root user which interferes 
+  #   with makepkg use of fakeroot
+  patch -p1 -i $srcdir/ngs.patch 
+  patch -p1 -i $srcdir/ngs-python.patch 
+}
+
+build(){
+  cd "${_pkgname}-${pkgver}"
+  ./configure --prefix="$pkgdir/usr/" --build-prefix="$srcdir/build"
+  cd ./ngs-python
+  ./configure --prefix="$pkgdir/usr/" --build-prefix="$srcdir/build" --with-ngs-sdk-prefix="/usr" --with-ncbi-vdb-prefix="/usr"
+  cd ../
+  make -C ngs-sdk
+  make -C ngs-python
+}
+
+#check(){
+#  cd "${pkgname}-${pkgver}"
+#  make -k test
+#}
+
+package(){
+  cd "$_pkgname-$pkgver"
+  # ncbi does not use autoconf/automake so there is no respect for DESTDIR
+  #   but there is a ROOT(dir)
+  #make "ROOT=$pkgdir" install
+  make -C ngs-python install
+
+  # add license
+  mkdir -p "$pkgdir/usr/share/licenses/${pkgname}"
+  cp "LICENSE" "$pkgdir/usr/share/licenses/${pkgname}/LICENSE"
+}
diff --git a/ngs-python.patch b/ngs-python.patch
new file mode 100644
index 000000000000..4d5f49c7e470
--- /dev/null
+++ b/ngs-python.patch
@@ -0,0 +1,30 @@
+--- a/ngs-python/setup.py	2019-03-18 12:37:12.000000000 -0400
++++ b/ngs-python/setup.py	2019-05-28 13:09:44.344531737 -0400
+@@ -17,7 +17,6 @@
+       author='sra-tools',
+       author_email='sra-tools@ncbi.nlm.nih.gov',
+       packages=['ngs'],
+-      include_package_data=True,
+       scripts=[],
+       #test_suite="tests",
+       )
+
+--- a/ngs-python/Makefile.python	2019-05-28 13:42:40.144181446 -0400
++++ b/ngs-python/Makefile.python	2019-05-28 13:41:25.357950185 -0400
+@@ -79,14 +79,8 @@
+ 	@ mkdir -p $@
+ 
+ install: $(TARGETS) $(INST_PYTHONDIR) copyexamples
+-ifeq (0, $(shell id -u))
+-	@ echo "Installing ngs package..."
+-	@ python setup.py -q install --root="$pkgdir/"
+-   
+-else
+-	@ echo "Installing ngs package..."
+-	@ python setup.py -q install --user
+-endif
++	@ echo "Installing ngs package..." 
++	@ python setup.py -q install --root=$(subst usr/,,$(INST_PYTHONDIR))
+ 
+ ifneq (, $(NGS_LIBDIR))
+ ifneq (, $(VDB_LIBDIR))
diff --git a/ngs.patch b/ngs.patch
new file mode 100644
index 000000000000..27bcb5497b44
--- /dev/null
+++ b/ngs.patch
@@ -0,0 +1,65 @@
+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/
+ 
+-ifeq (linux, $(OS))
+-    ifeq (0, $(shell id -u))
+-        LINUX_ROOT = true
+-        DOC_TARGET = $(ROOT)/usr/local/share/doc/ngs/
+-    endif
+-endif
++#ifeq (linux, $(OS))
++#    ifeq (0, $(shell id -u))
++#        LINUX_ROOT = true
++#        DOC_TARGET = $(ROOT)/usr/local/share/doc/ngs/
++#    endif
++#endif
++LINUX_ROOT = false
+ 
+ install: $(TARGETS) $(INST_JARDIR) $(INST_JARDIR)/ngs-java.jar.$(VERSION) copydocs copyexamples 
+ ifeq (true, $(LINUX_ROOT))
+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, $(shell id -u))
+ 	@ echo "Installing ngs-python package..."
+-	@ python setup.py -q install
++	@ python setup.py -q install --root="$pkgdir/"
+  
+ else
+ 	@ echo "Installing ngs-python package..."
+@@ -78,7 +78,7 @@
+ install: $(TARGETS) $(INST_PYTHONDIR) copyexamples
+ ifeq (0, $(shell id -u))
+ 	@ echo "Installing ngs package..."
+-	@ python setup.py -q install
++	@ python setup.py -q install --root="$pkgdir/"
+    
+ else
+ 	@ echo "Installing ngs package..."
+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
+ 
+-ifeq (linux, $(OS))
+-    ifeq (0, $(shell id -u))
+-        LINUX_ROOT = true
+-    endif
+-endif
++#ifeq (linux, $(OS))
++#    ifeq (0, $(shell id -u))
++#        LINUX_ROOT = true
++#    endif
++#endif
++LINUX_ROOT = false
+ 
+ install: copylibs copyincludes copyexamples
+ ifeq (true, $(LINUX_ROOT))