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Add the cd-hit program to the binaries

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Former-commit-id: 0ecdb8d90e9e78940ec9b109c3a0b484bcacf14d
Former-commit-id: 4c3551f7bca6c203fb7ffbba6c2e37d15d763487
This commit is contained in:
Eric Coissac
2016-01-27 13:09:43 +01:00
parent 647695d2a2
commit b2cc474077
5 changed files with 89 additions and 1 deletions
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1
.gitignore vendored Normal file
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@ -0,0 +1 @@
/test/

3
src/Makefile
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@ -30,7 +30,8 @@ DIRS = aragorn \
sumaclust \
sumatra \
gawk \
getopt
getopt \
cd-hit
include ../config/targets/propagate.targ

26
src/cd-hit/Makefile Normal file
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# ---------------------------------------------------------------
# $Id: $
# ---------------------------------------------------------------
# @file: Makefile
# @desc: makefile for package exonerate
#
# @history:
# @+ <Gloup> : Sept 15 : Adapted to ORG.Annot
#
# @note: should be processed with gnu compatible make
# @note: helixware_compatible
#
# @end:
# ---------------------------------------------------------------
#
include ../../config/auto.conf
PKG = cd-hit-v4.6.4-2015-0603
MAKEOPTIONS= openmp=no PREFIX=$(PRTPATH)/bin
include $(CFGDIR)targets/package.targ
include $(CFGDIR)targets/help.targ

BIN
src/cd-hit/cd-hit-v4.6.4-2015-0603.tgz Normal file
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60
src/muscle/muscle3.8.31/muscle.make.stderr.txt
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alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
switch (Alpha)
^
1 warning generated.
clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
switch (m_JoinStyle)
^
clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
switch (m_CentroidStyle)
^
clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
switch (m_JoinStyle)
^
3 warnings generated.
glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
switch (g_PPScore)
^
1 warning generated.
msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
switch (Method)
^
1 warning generated.
objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch]
switch (OS)
^
1 warning generated.
objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
switch (g_TermGaps)
^
1 warning generated.
params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
switch (g_PPScore)
^
1 warning generated.
In file included from profdb.cpp:9:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
switch(m_Distance)
^
1 warning generated.
profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
switch (g_Alpha)
^
1 warning generated.
In file included from refine.cpp:9:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
switch(m_Distance)
^
1 warning generated.
subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
for (unsigned i = 0; i < uNodeCount; ++i)
~ ^ ~~~~~~~~~~
1 warning generated.
In file included from treefrommsa.cpp:5:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
switch(m_Distance)
^
1 warning generated.