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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.patch43
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()