diff options
Diffstat (limited to 'sci-biology/amos/files')
| -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() |