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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-09-11 16:09:28 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-09-11 16:09:28 +0200 |
| commit | 5e6e183d8bca94b14d155524d8feeaaf4286e7dd (patch) | |
| tree | 06ad1aaef68fc427f282e0b62e755c94e7099730 /sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch | |
| parent | sci-biology/jellyfish: remove doubled econf call (diff) | |
| download | sci-5e6e183d8bca94b14d155524d8feeaaf4286e7dd.tar.gz sci-5e6e183d8bca94b14d155524d8feeaaf4286e7dd.tar.bz2 sci-5e6e183d8bca94b14d155524d8feeaaf4286e7dd.zip | |
sci-biology/amos: adjust to SLOTed jellyfish and drop qt4
Jellyfish resides in ${EPREFIX}/usr/include/jellyfish1/ now.
The package needed qt4 with qt3support enabled to compile
hawkeye utility. Let's try with qt5 core only.
Also enabling compilation of all utilities if they pass
configure checks.
Currently, jellyfish linking fails with some cxx linking error,
maybe my -lm or -lpthreads needs to be recompiled with gcc-8.2.0
too? Also, boot is somehow not picked up.
Bug: https://bugs.gentoo.org/show_bug.cgi?id=663110
Package-Manager: Portage-2.3.48, Repoman-2.3.10
Diffstat (limited to 'sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch')
| -rw-r--r-- | sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch new file mode 100644 index 000000000..4b52c5640 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch @@ -0,0 +1,43 @@ +--- config/amos.m4 2018-09-11 13:23:14.478444129 +0200 ++++ config/amos.m4 2018-09-11 13:36:36.697612245 +0200 +@@ -695,15 +695,15 @@ + else + jellyfish_unspecified=no + fi +-if ! test -f "$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() |