From 5e6e183d8bca94b14d155524d8feeaaf4286e7dd Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue, 11 Sep 2018 16:09:28 +0200
Subject: sci-biology/amos: adjust to SLOTed jellyfish and drop qt4

Jellyfish resides in ${EPREFIX}/usr/include/jellyfish1/ now.

The package needed qt4 with qt3support enabled to compile
hawkeye utility. Let's try with qt5 core only.

Also enabling compilation of all utilities if they pass
configure checks.

Currently, jellyfish linking fails with some cxx linking error,
maybe my -lm or -lpthreads needs to be recompiled with gcc-8.2.0
too? Also, boot is somehow not picked up.

Bug: https://bugs.gentoo.org/show_bug.cgi?id=663110
Package-Manager: Portage-2.3.48, Repoman-2.3.10
---
 .../files/amos-3.1.0-rename_to_jellyfish1.patch    | 43 ++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch

(limited to 'sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch')

diff --git a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch
new file mode 100644
index 000000000..4b52c5640
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch
@@ -0,0 +1,43 @@
+--- config/amos.m4	2018-09-11 13:23:14.478444129 +0200
++++ config/amos.m4	2018-09-11 13:36:36.697612245 +0200
+@@ -695,15 +695,15 @@
+ else
+ 	jellyfish_unspecified=no
+ fi
+-if ! test -f "$jellyfish_dir/jellyfish/mer_counting.hpp"; then
++if ! test -f "$jellyfish_dir/jellyfish1/mer_counting.hpp"; then
+ 	if test $jellyfish_unspecified = no; then
+-		AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish/compacted_hash.hpp"])
++		AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish1/compacted_hash.hpp"])
+ 	fi
+ 	JELLYFISH_LDADD=
+ 	JELLYFISH_CPPFLAGS=
+ 	AC_MSG_RESULT([not found])
+ else
+-	JELLYFISH_LDADD="-ljellyfish -lpthread"
++	JELLYFISH_LDADD="-ljellyfish-1.1 -lpthread"
+ 	JELLYFISH_CPPFLAGS="-I $jellyfish_dir"
+ 	AC_DEFINE([WITH_JELLYFISH], [1], [Define to 1 if using Jellyfish])
+ 	cppflags_save="$CPPFLAGS"
+@@ -715,7 +715,7 @@
+ 	AC_LANG_PUSH([C++])
+ 	AC_LINK_IFELSE([
+ 		AC_LANG_PROGRAM([
+-#include <jellyfish/mer_counting.hpp>
++#include <jellyfish1/mer_counting.hpp>
+ #include <string>
+ 	], [
+ std::string s;
+--- src/Align/kmer-cov-plot.cc	2018-09-11 13:23:15.079443556 +0200
++++ src/Align/kmer-cov-plot.cc	2018-09-11 13:36:36.831612096 +0200
+@@ -388,8 +388,8 @@
+ 
+ #ifdef WITH_JELLYFISH
+ 
+-#include <jellyfish/compacted_hash.hpp>
+-#include <jellyfish/mer_counting.hpp>
++#include <jellyfish1/compacted_hash.hpp>
++#include <jellyfish1/mer_counting.hpp>
+ 
+ // Assert that jellyfish is using the expected kmer representation
+ static void jellyfish_check()
-- 
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