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- children = ( - A74D3655137DAB8300332B0C /* addtargets2.cpp */, - A74D3656137DAB8300332B0C /* alignchime.cpp */, - A74D3657137DAB8300332B0C /* alignchimel.cpp */, - A74D3658137DAB8300332B0C /* allocs.h */, - A74D3659137DAB8300332B0C /* alnheuristics.h */, - A74D365A137DAB8300332B0C /* alnparams.cpp */, - A74D365B137DAB8300332B0C /* alnparams.h */, - A74D365C137DAB8300332B0C /* alpha.cpp */, - A74D365D137DAB8300332B0C /* alpha.h */, - A74D365E137DAB8300332B0C /* alpha2.cpp */, - A74D365F137DAB8300332B0C /* chainer.h */, - A74D3660137DAB8300332B0C /* chime.h */, - A74D3661137DAB8300332B0C /* diagbox.h */, - A74D3662137DAB8300332B0C /* dp.h */, - A74D3663137DAB8300332B0C /* evalue.h */, - A74D3664137DAB8300332B0C /* fractid.cpp */, - A74D3665137DAB8300332B0C /* getparents.cpp */, - A74D3666137DAB8300332B0C /* globalalign2.cpp */, - A74D3667137DAB8300332B0C /* help.h */, - A74D3668137DAB8300332B0C /* hsp.h */, - A74D3669137DAB8300332B0C /* hspfinder.h */, - A74D366A137DAB8300332B0C /* make3way.cpp */, - A74D366B137DAB8300332B0C /* mx.cpp */, - A74D366C137DAB8300332B0C /* mx.h */, - A74D366D137DAB8300332B0C /* myopts.h */, - A74D366E137DAB8300332B0C /* myutils.cpp */, - A74D366F137DAB8300332B0C /* myutils.h */, - A74D3670137DAB8300332B0C /* orf.h */, - A74D3671137DAB8300332B0C /* out.h */, - A74D3672137DAB8300332B0C /* path.cpp */, - A74D3673137DAB8300332B0C /* path.h */, - A74D3674137DAB8300332B0C /* searchchime.cpp */, - A74D3675137DAB8300332B0C /* seq.h */, - A74D3676137DAB8300332B0C /* seqdb.cpp */, - A74D3677137DAB8300332B0C /* seqdb.h */, - A74D3678137DAB8300332B0C /* setnucmx.cpp */, - A74D3679137DAB8300332B0C /* sfasta.cpp */, - A74D367A137DAB8300332B0C /* sfasta.h */, - A74D367B137DAB8300332B0C /* svnmods.h */, - A74D367C137DAB8300332B0C /* svnversion.h */, - A74D367D137DAB8300332B0C /* timers.h */, - A74D367E137DAB8300332B0C /* timing.h */, - A74D367F137DAB8300332B0C /* tracebackbit.cpp */, - A74D3680137DAB8300332B0C /* uc.h */, - A74D3681137DAB8300332B0C /* uchime_main.cpp */, - A74D3682137DAB8300332B0C /* ultra.h */, - A74D3683137DAB8300332B0C /* usort.cpp */, - A74D3684137DAB8300332B0C /* viterbifast.cpp */, - A74D3685137DAB8300332B0C /* windex.h */, - A74D3686137DAB8300332B0C /* writechhit.cpp */, - ); - name = uchime; - sourceTree = ""; - }; A7D161E7149F7F50000523E8 /* fortran */ = { isa = PBXGroup; children = ( @@ -1302,6 +1191,8 @@ isa = PBXGroup; children = ( A7E9B6AE12D37EC400DA6239 /* command.hpp */, + 219C1DE11552C508004209F9 /* newcommandtemplate.h */, + 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7A61F2B130062E000E05B6B /* amovacommand.h */, @@ -1376,6 +1267,8 @@ A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */, A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */, + 219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */, + 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */, A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, @@ -1384,6 +1277,8 @@ A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A70056E8156A93E300924A2D /* getotulabelscommand.h */, + A70056E5156A93D000924A2D /* getotulabelscommand.cpp */, A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, @@ -1416,12 +1311,16 @@ A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7A0671C156294810095C8C5 /* listotulabelscommand.h */, + A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, A7FA10001302E096003860FE /* mantelcommand.h */, A7FA10011302E096003860FE /* mantelcommand.cpp */, A724D2B4153C8600000A826F /* makebiomcommand.h */, A724D2B6153C8628000A826F /* makebiomcommand.cpp */, + A7A0671D1562AC230095C8C5 /* makecontigscommand.h */, + A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */, A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, @@ -1486,6 +1385,8 @@ A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A70056E9156AB6D400924A2D /* removeotulabelscommand.h */, + A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */, A727864212E9E28C00F86ABA /* removerarecommand.h */, A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, @@ -1795,7 +1696,6 @@ A7E9BA4512D3965600DA6239 /* chimera */ = { isa = PBXGroup; children = ( - A74D3644137DA7CE00332B0C /* uchime */, A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */, A7E9B65D12D37EC300DA6239 /* bellerophon.h */, A7E9B67412D37EC400DA6239 /* ccode.cpp */, @@ -1929,7 +1829,7 @@ name = Mothur; productInstallPath = "$(HOME)/bin"; productName = mothur; - productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; + productReference = 8DD76FB20486AB0100D96B5E /* mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -2245,28 +2145,6 @@ A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */, A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */, A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */, - A74D3687137DAB8300332B0C /* addtargets2.cpp in Sources */, - A74D3688137DAB8400332B0C /* alignchime.cpp in Sources */, - A74D3689137DAB8400332B0C /* alignchimel.cpp in Sources */, - A74D368A137DAB8400332B0C /* alnparams.cpp in Sources */, - A74D368B137DAB8400332B0C /* alpha.cpp in Sources */, - A74D368C137DAB8400332B0C /* alpha2.cpp in Sources */, - A74D368D137DAB8400332B0C /* fractid.cpp in Sources */, - A74D368E137DAB8400332B0C /* getparents.cpp in Sources */, - A74D368F137DAB8400332B0C /* globalalign2.cpp in Sources */, - A74D3690137DAB8400332B0C /* make3way.cpp in Sources */, - A74D3691137DAB8400332B0C /* mx.cpp in Sources */, - A74D3692137DAB8400332B0C /* myutils.cpp in Sources */, - A74D3693137DAB8400332B0C /* path.cpp in Sources */, - A74D3694137DAB8400332B0C /* searchchime.cpp in Sources */, - A74D3695137DAB8400332B0C /* seqdb.cpp in Sources */, - A74D3696137DAB8400332B0C /* setnucmx.cpp in Sources */, - A74D3697137DAB8400332B0C /* sfasta.cpp in Sources */, - A74D3698137DAB8400332B0C /* tracebackbit.cpp in Sources */, - A74D3699137DAB8400332B0C /* uchime_main.cpp in Sources */, - A74D369A137DAB8400332B0C /* usort.cpp in Sources */, - A74D369B137DAB8400332B0C /* viterbifast.cpp in Sources */, - A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */, A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */, A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */, A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */, @@ -2308,6 +2186,12 @@ A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */, A7D755DA1535F679009BF21A /* treereader.cpp in Sources */, A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */, + 219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */, + 219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */, + A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */, + A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */, + A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */, + A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -2319,12 +2203,13 @@ buildSettings = { ALWAYS_SEARCH_USER_PATHS = NO; COPY_PHASE_STRIP = NO; + DEPLOYMENT_LOCATION = YES; GCC_DYNAMIC_NO_PIC = NO; GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; - INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; SDKROOT = macosx10.6; + SKIP_INSTALL = NO; }; name = Debug; }; @@ -2336,8 +2221,8 @@ DEPLOYMENT_LOCATION = YES; GCC_MODEL_TUNING = G5; GCC_WARN_UNUSED_VALUE = YES; - INSTALL_PATH = ./; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; + SKIP_INSTALL = NO; }; name = Release; }; @@ -2353,15 +2238,15 @@ GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.24.0\\\"\"", - "RELEASE_DATE=\"\\\"3/12/2012\\\"\"", + "VERSION=\"\\\"1.25.0\\\"\"", + "RELEASE_DATE=\"\\\"5/01/2012\\\"\"", ); "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; HEADER_SEARCH_PATHS = ""; - INSTALL_PATH = ""; + INSTALL_PATH = TARGET_BUILD_DIR; MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( @@ -2374,6 +2259,7 @@ "-lreadline", ); SDKROOT = macosx10.6; + SKIP_INSTALL = NO; USER_HEADER_SEARCH_PATHS = ""; }; name = Debug; @@ -2399,7 +2285,7 @@ GCC_WARN_UNUSED_PARAMETER = YES; GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; - INSTALL_PATH = ""; + INSTALL_PATH = TARGET_BUILD_DIR; MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", @@ -2411,6 +2297,7 @@ "-lreadline", ); SDKROOT = macosx10.6; + SKIP_INSTALL = NO; }; name = Release; };