sci-biology/SPAdes: fix compile issue but drop KEYWORDS because of QA issues

Use patch from https://github.com/Homebrew/homebrew-science/pull/5616
The package install its own *.py files outside of PYTHON's site-packages/.
The "make install" procedure is flakey shellscript and there is no setup.py so we could
reuse common infrastructure for pythonic packages.
There are plenty of bundled 3rd-party apps, some of them compiling statically.

Package-Manager: Portage-2.3.5, Repoman-2.3.2

3 files changed, 49 insertions, 10 deletions

diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index 68d64dea5..d97eb1723 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,5 +1,5 @@
 DIST SPAdes-3.10.1.tar.gz 7293511 SHA256 d49dd9eb947767a14a9896072a1bce107fb8bf39ed64133a9e2f24fb1f240d96 SHA512 0d1bfaa67d6fc8732bc8d5ee4994629e95296a2a6c49bbc73383a7bdd7586f9be6ea6e2ffe3160821f7bd7c31745434fe5f6319da756ded3275fb6650ae9ada9 WHIRLPOOL c1dfb58411a38422122914b242361d2f3822e89c1456fa8abfb3ec46785808ff58306521edb2fee02f655404ba449d74643dcdfbecb39b67eaa0aba026f1f9a0
 DIST SPAdes-3.10.1_dipspades_manual.html 12561 SHA256 c4240cd2f8e29e428be03a76080b8d7b1360a5d4e2034472df43f435319b5e1c SHA512 618284c899b5c0f167b91638ac3ca4d7ee2c932f5acbfa6225f43276b073259000022f12afa3d8df26dfd967085b3d2d11ca006766169199afc02de111a78db4 WHIRLPOOL 0fa1a38523c23d32efbb4af9a16d49cf25a19b3f13a429ee2f926c04865d969fbf6b99410cf188669206d4600423f50a56143f915c1c24d837774e9cf1203505
 DIST SPAdes-3.10.1_manual.html 60105 SHA256 14c8fba956c8c70f1d72950a8b171395d4bca65feb89c9be20a723f8ae92f2c3 SHA512 ce69945b00eee73a4384b284fcd66e3d9f0619cf9c3eb76311604ba749841fe5b56208fcd2fdd02455567ad3c0125312dc80f67d69137c66f8805c709f39041c WHIRLPOOL 8131280813e4e581c182eccb8910371ee297ebe31824cfa20f9ed0c3dbfbdce5a8ffe63625454297a88fd57df0fe12509d731654407513ad4dfc3d239bd77842
-DIST SPAdes-3.10.1_rnaspades_manual.html 3725 SHA256 f9d76febea6e58e8c935b7e50febcb36516643513400723436d5b46875d97a40 SHA512 03fc591f78ea09436e53896c6c31fae195ee11d2eca74f57ea80b366e6a71b969f6e60bf96cbf5e948a1d708b14041f803c1987b3f918585d867b8f66d85d0dd WHIRLPOOL 68895b8ad097e681592ecc6a337ba5e4ebed627bc4a99a4fea1801634c3ea98379dece96a347f8ff755a7d84d44ef1e187306401dc6a93d19e1ac707fa6204b2
+DIST SPAdes-3.10.1_rnaspades_manual.html 4676 SHA256 8a8fa4ee73339a9d64325aba6fe901dcafac1dca9b503388563753fa5f764efe SHA512 68d5dc92c6bc7c865221d52a45d056657cf80ecb4a3d25f49b68ad6e654d353372e9ce862dbf9c164da310a703a31e81f5af68b8ceab1d64651134650fce4cff WHIRLPOOL 4633b5befa1978845d10ff43b4798c9353317e23106ddd936a045a51777c8f7793bacfb76e799e944c8f709d6d7313d36e88f486cdded9555f7bef3c74199f1d
 DIST SPAdes-3.10.1_truspades_manual.html 10769 SHA256 eb8b40beb331eca3d8fd394cd0ce2237a8b6d0245f63ba2735bdacd5bcf5858a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b WHIRLPOOL 9f5f863ddf65ceca70021948459a8a492f90bc879870d11a04ef85c510574239ab0ad1139bca8a835c7df9c785599385dff5657ec68174a67617bb8e77c53a87
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index 36f724d83..73050c1e4 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -12,13 +12,13 @@ HOMEPAGE="http://bioinf.spbau.ru/en/spades"
 SRC_URI="
 	http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
 	http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html
-	http://spades.bioinf.spbau.ru/release3.9.1/dipspades_manual.html -> ${P}_dipspades_manual.html
-	http://spades.bioinf.spbau.ru/release3.9.1/rnaspades_manual.html -> ${P}_rnaspades_manual.html
-	http://spades.bioinf.spbau.ru/release3.9.1/truspades_manual.html -> ${P}_truspades_manual.html"
+	http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html
+	http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+	http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE=""
 
 DEPEND="
@@ -28,6 +28,26 @@ DEPEND="
 	dev-libs/boost"
 RDEPEND="${DEPEND}"
 
+# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
+#      existing packages
+# nlopt
+# llvm
+# python_libs
+# bamtools
+# ConsensusCore
+# ssw
+# jemalloc
+# htrie
+# getopt_pp
+# cppformat
+# cityhash
+# samtools
+# bwa
+
+# BUG: "${S}"/ext/tools/ contains even two version of bwa
+# bwa-0.7.12
+# bwa-0.6.2
+
 pkg_pretend() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
 		if [[ $(tc-getCXX) == *g++ ]] ; then
@@ -39,13 +59,22 @@ pkg_pretend() {
 	fi
 }
 
-#src_compile(){
-#	# grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts
-#	PREFIX="${D}"/usr ./spades_compile.sh || die
-#}
+src_prepare(){
+	# https://github.com/Homebrew/homebrew-science/pull/5616
+	epatch "${FILESDIR}"/"${P}"-fix-missing-include.patch
+	cp -p spades_compile.sh spades_install.sh || die
+	sed -e 's/make install/#make install/;s/cd $PREFIX/#cd $PREFIX/' -i spades_compile.sh || die
+	default
+}
+
+src_compile(){
+	# grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts
+	PREFIX="${D}"/usr ./spades_compile.sh || die
+}
 
 src_install(){
-	PREFIX="${ED}"/usr ./spades_compile.sh || die
+	PREFIX="${ED}"/usr sh ./spades_install.sh || die
+	# BUG: move *.py files to standard site-packages/ subdirectories
 	insinto /usr/share/"${PN}"
 	dodoc "${DISTDIR}"/${P}_*manual.html
 }
diff --git a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
new file mode 100644
index 000000000..bb6d75797
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
@@ -0,0 +1,10 @@
+--- SPAdes-3.10.1/src/common/utils/segfault_handler.hpp.ori	2017-05-13 22:43:01.296207276 +0200
++++ SPAdes-3.10.1/src/common/utils/segfault_handler.hpp	2017-05-13 22:43:41.437310225 +0200
+@@ -12,6 +12,7 @@
+ #include "boost/noncopyable.hpp"
+ 
+ #include <signal.h>
++#include <functional>
+ 
+ struct segfault_handler : boost::noncopyable {
+     typedef std::function<void()> callback_t;