proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 332 insertions, 0 deletions

diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
new file mode 100644
index 000000000000..08824f51b1cc
--- /dev/null
+++ b/sci-biology/velvet/Manifest
@@ -0,0 +1,2 @@
+DIST velvet_1.0.18.tgz 7598196 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad WHIRLPOOL 69dcb5a6760b66eba65d054562e873d2c000dc57b487cdcf2c977bc1c0106bf027a79ff3b7e81da8a0f82b00635b755c26135b34de51cae34f4d276f15c2be74
+DIST velvet_1.2.10.tgz 18818559 SHA256 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 WHIRLPOOL 595e40c92ab5724b3e9a5af11f023307da7c66628b0c96d2ac2c89617e2aaa8a84279252c397f52d4603119d6fcb4995d2bf6e38f7de8c7c9616bde3aefdcd64
diff --git a/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff
new file mode 100644
index 000000000000..883211a557d6
--- /dev/null
+++ b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff
@@ -0,0 +1,126 @@
+Debundle zlib, fixes parallel build, respect user FLAGS
+
+--- src/readSet.c
++++ src/readSet.c
+@@ -23,18 +23,13 @@
+ #include <string.h>
+ #include <math.h>
+ #include <time.h>
++#include <zlib.h>
+ 
+ #include "globals.h"
+ #include "tightString.h"
+ #include "readSet.h"
+ #include "utility.h"
+ 
+-#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+-#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+-#else
+-#include "../third-party/zlib-1.2.3/zlib.h"
+-#endif
+-
+ #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+ #  include <fcntl.h>
+ #  include <io.h>
+
+--- Makefile
++++ Makefile
+@@ -1,77 +1,62 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
+-LDFLAGS = -lm
+-OPT = -O3
++LIBS = -lm -lz
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+ 
+-Z_LIB_DIR=third-party/zlib-1.2.3
+-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
+-
+-# Mac OS users: uncomment the following lines
+-# Z_LIB_FILES=
+-# LDFLAGS = -lm -lz
+-# CFLAGS = -Wall -m64
+-
+-# Sparc/Solaris users: uncomment the following line
+-# CFLAGS = -Wall -m64
+-
+ OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
++OBJDE  = $(subst obj,objde,$(OBJ))
+ 
+-default : cleanobj zlib obj velveth velvetg doc
++default : cleanobj  obj velveth velvetg 
+ 
+ clean :
+-	-rm obj/*.o obj/dbg/*.o ./velvet* 
+-	cd $(Z_LIB_DIR) && make clean
++	-rm -f obj/*.o obj/dbg/*.o ./velvet* objde/*.o
+ 	-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
+ 
+ cleanobj: 
+-	-rm obj/*.o obj/dbg/*.o 
+-
+-zlib : 
+-	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++	-rm -f obj/*.o obj/dbg/*.o objde/*.o
+ 
+ velveth : obj 
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(LIBS)
+ 
+ 
+ velvetg : obj
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(LIBS)
+ 
+ debug : cleanobj obj/dbg
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
+ 
+ color : cleanobj obj_de
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de objde/tightString.o objde/run.o objde/recycleBin.o objde/splay.o objde/splayTable.o objde/readSet.o objde/crc.o objde/utility.o objde/kmer.o $(LIBS)
++	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de objde/tightString.o objde/graph.o objde/run2.o objde/fibHeap.o objde/fib.o objde/concatenatedGraph.o objde/passageMarker.o objde/graphStats.o objde/correctedGraph.o objde/dfib.o objde/dfibHeap.o objde/recycleBin.o objde/readSet.o objde/shortReadPairs.o objde/scaffold.o objde/locallyCorrectedGraph.o objde/graphReConstruction.o objde/roadMap.o objde/preGraph.o objde/preGraphConstruction.o objde/concatenatedPreGraph.o objde/readCoherentGraph.o objde/utility.o objde/kmer.o $(LIBS)
+ 
+ colordebug : cleanobj obj/dbg_de
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de objde/dbg/tightString.o objde/dbg/run.o objde/dbg/recycleBin.o objde/dbg/splay.o objde/dbg/splayTable.o objde/dbg/readSet.o objde/dbg/crc.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de objde/dbg/tightString.o objde/dbg/graph.o objde/dbg/run2.o objde/dbg/fibHeap.o objde/dbg/fib.o objde/dbg/concatenatedGraph.o objde/dbg/passageMarker.o objde/dbg/graphStats.o objde/dbg/correctedGraph.o objde/dbg/dfib.o objde/dbg/dfibHeap.o objde/dbg/recycleBin.o objde/dbg/readSet.o objde/dbg/shortReadPairs.o objde/dbg/scaffold.o objde/dbg/locallyCorrectedGraph.o objde/dbg/graphReConstruction.o objde/dbg/roadMap.o objde/dbg/preGraph.o objde/dbg/preGraphConstruction.o objde/dbg/concatenatedPreGraph.o objde/dbg/readCoherentGraph.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
+ 
+ objdir:
+ 	mkdir -p obj
++	mkdir -p objde
+ 
+-obj: zlib objdir $(OBJ)
++obj:  objdir $(OBJ)
+ 
+-obj_de: override DEF := $(DEF) -D COLOR
+-obj_de: zlib cleanobj objdir $(OBJ)
++obj_de:  cleanobj objdir $(OBJDE)
+ 
+ obj/dbgdir: 
+ 	mkdir -p obj/dbg
+ 
+-obj/dbg: zlib obj/dbgdir $(OBJDBG)
++obj/dbg: obj/dbgdir $(OBJDBG)
+ 
+ obj/dbg_de: override DEF := $(DEF) -D COLOR
+-obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
++obj/dbg_de: cleanobj obj/dbgdir $(OBJDBG)
+ 
+ obj/%.o: src/%.c
+ 	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
+ 
++objde/%.o: src/%.c
++	$(CC) $(CFLAGS) $(OPT) $(DEF) -D COLOR -c $? -o $@ 
++
+ obj/dbg/%.o: src/%.c
+ 	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
+ 
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
new file mode 100644
index 000000000000..ed53a1229b5b
--- /dev/null
+++ b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
@@ -0,0 +1,72 @@
+diff -durr Makefile Makefile
+--- Makefile	2011-01-27 16:52:58.853408562 +0000
++++ Makefile	2011-01-27 17:01:45.088065521 +0000
+@@ -1,8 +1,4 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
+-LDFLAGS = -lm
+-OPT = -O3
++LIBS = -lm -lz
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+@@ -41,29 +37,29 @@
+ 	-rm obj/*.o obj/dbg/*.o 
+ 
+ zlib : 
+-	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++	echo "unbundled zlib"
+ 
+ velveth : obj 
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(LIBS) 
+ 
+ 
+ velvetg : obj
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS)
+ 
+ debug : override DEF := $(DEF) -D DEBUG 
+ debug : cleanobj obj/dbg
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
+ 
+ color : override DEF := $(DEF) -D COLOR
+ color : cleanobj obj_de
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) 
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) 
+ 
+ colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
+ colordebug : cleanobj obj/dbg_de
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
+ 
+ objdir:
+ 	mkdir -p obj
+@@ -83,7 +79,7 @@
+ obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
+ 
+ obj/%.o: src/%.c
+-	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
++	$(CC) $(CFLAGS)  $(DEF) -c $? -o $@ 
+ 
+ obj/dbg/%.o: src/%.c
+ 	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
+diff -durr src/readSet.c src/readSet.c
+--- src/readSet.c	2011-01-27 16:52:58.804084948 +0000
++++ src/readSet.c	2011-01-27 17:02:55.380324786 +0000
+@@ -24,6 +24,7 @@
+ #include <math.h>
+ #include <time.h>
+ #include <limits.h>
++#include <zlib.h>
+ 
+ #include "globals.h"
+ #include "tightString.h"
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/velvet/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
new file mode 100644
index 000000000000..c0bfb929033e
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs flag-o-matic
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="-doc"
+KEYWORDS="amd64 x86"
+
+RDEPEND="sys-libs/zlib"
+DEPEND="${RDEPEND}
+	doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+	# necessary?
+	# append-flags -O3 # as recommended by upstream
+	epatch "${FILESDIR}"/${P}-gentoo-r1.diff
+	use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+}
+
+src_compile() {
+	tc-export CC
+	MAKE_XOPTS=""
+	if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
+	if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
+	emake -j1 $MAKE_XOPTS || die
+	emake -j1 $MAKE_XOPTS color || die
+}
+
+src_install() {
+	dobin velvet{g,h,g_de,h_de} || die
+	insinto /usr/share/${PN}
+	doins -r contrib || die
+	dodoc Manual.pdf CREDITS.txt ChangeLog || die
+}
+
+pkg_postinst() {
+	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+	elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+	elog "	VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+}
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
new file mode 100644
index 000000000000..86b06ffcd125
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc openmp"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+	if ! use doc; then
+		sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+	fi
+	elog "Upstream recommendes using -O3 in CFLAGS"
+	echo
+	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+	elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+	elog "  VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+	MAKEOPTS+=" -j1"
+
+	if [[ $(tc-getCC) =~ gcc ]]; then
+		local eopenmp=-fopenmp
+	elif [[ $(tc-getCC) =~ icc ]]; then
+		local eopenmp=-openmp
+	else
+		elog "Cannot detect compiler type so not setting openmp support"
+	fi
+	append-flags -fPIC ${eopenmp}
+	append-ldflags ${eopenmp}
+
+	tc-export CC
+
+	MAKE_XOPTS=(
+		CC=$(tc-getCC)
+		CFLAGS="${CFLAGS}"
+		OPT="${CFLAGS}"
+	)
+	if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
+	if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
+}
+
+src_compile() {
+	emake "${MAKE_XOPTS[@]}"
+	emake "${MAKE_XOPTS[@]}" color
+}
+
+src_test() {
+	emake "${MAKE_XOPTS[@]}" test
+}
+
+src_install() {
+	dobin velvet{g,h,g_de,h_de}
+	insinto /usr/share/${PN}
+	doins -r contrib
+	dodoc Manual.pdf CREDITS.txt ChangeLog
+}