sci-biology/bowtie: version bump, SLOT major version

sci-biology/bowtie is now SLOTed, in order to allow for a
parallel installation with bowtie2. In addition, the latest
bowtie now supports dev-cpp/tbb with 'tbb' USE flag.

2 files changed, 14 insertions, 45 deletions

diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
deleted file mode 100644
index 3c8a1e1d9ca4..000000000000
--- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- alphabet.h |   24 ++++++++++++------------
- 1 files changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/alphabet.h b/alphabet.h
-index b464ddf..08d0281 100644
---- a/alphabet.h
-+++ b/alphabet.h
-@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
- 	return s_rc;
- }
- 
-+/// Reverse a string in-place
-+template <typename TStr>
-+static inline void reverseInPlace(TStr& s) {
-+	typedef typename Value<TStr>::Type TVal;
-+	size_t len = length(s);
-+	for(size_t i = 0; i < (len>>1); i++) {
-+		TVal tmp = s[i];
-+		s[i] = s[len-i-1];
-+		s[len-i-1] = tmp;
-+	}
-+}
-+
- /**
-  * Reverse-complement s in-place.  Ns go to Ns.
-  */
-@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
- 	}
- }
- 
--/// Reverse a string in-place
--template <typename TStr>
--static inline void reverseInPlace(TStr& s) {
--	typedef typename Value<TStr>::Type TVal;
--	size_t len = length(s);
--	for(size_t i = 0; i < (len>>1); i++) {
--		TVal tmp = s[i];
--		s[i] = s[len-i-1];
--		s[len-i-1] = tmp;
--	}
--}
--
- /**
-  * Return the reverse-complement of s.
-  */
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
new file mode 100644
index 000000000000..2a081ff297b8
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
@@ -0,0 +1,14 @@
+--- bowtie-1.1.2/Makefile
++++ bowtie-1.1.2/Makefile
+@@ -106,10 +106,7 @@
+ endif
+ 
+ OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
+-             edit.cpp ebwt.cpp
+-ifneq (1,$(WITH_TBB))
+-	OTHER_CPPS += tinythread.cpp
+-endif
++             edit.cpp ebwt.cpp tinythread.cpp
+ 
+ SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
+               log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \