diff options
author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
---|---|---|
committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/wise | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
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
Diffstat (limited to 'sci-biology/wise')
-rw-r--r-- | sci-biology/wise/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch | 301 | ||||
-rw-r--r-- | sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch | 407 | ||||
-rw-r--r-- | sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch | 302 | ||||
-rw-r--r-- | sci-biology/wise/files/wise-api.tex.patch | 38 | ||||
-rw-r--r-- | sci-biology/wise/files/wise-env | 1 | ||||
-rw-r--r-- | sci-biology/wise/metadata.xml | 5 | ||||
-rw-r--r-- | sci-biology/wise/wise-2.4.0_alpha.ebuild | 73 |
8 files changed, 1128 insertions, 0 deletions
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest new file mode 100644 index 000000000000..fc9cf9f0083c --- /dev/null +++ b/sci-biology/wise/Manifest @@ -0,0 +1 @@ +DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch new file mode 100644 index 000000000000..1ec433f19227 --- /dev/null +++ b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch @@ -0,0 +1,301 @@ +diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c +--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300 ++++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300 +@@ -213,7 +213,7 @@ + } + } + +-/* Function: getline() ++/* Function: get_line() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -377,7 +377,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -411,7 +411,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -438,7 +438,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -515,7 +515,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -555,12 +555,12 @@ + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) get_line(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -587,7 +587,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -636,7 +636,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -669,7 +669,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -816,7 +816,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -853,7 +853,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -949,7 +949,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch new file mode 100644 index 000000000000..d3c17098105e --- /dev/null +++ b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch @@ -0,0 +1,407 @@ +diff --git a/src/base/makefile b/src/base/makefile +index 4620f19..a84e2c7 100644 +--- a/src/base/makefile ++++ b/src/base/makefile +@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \ + + + #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++CFLAGS += -c -DUNIX -pthread ++LFLAGS = -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +diff --git a/src/corba/makefile b/src/corba/makefile +index df3dd78..237a1ba 100644 +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -1,10 +1,10 @@ + + +-CC = cc ++CC += gcc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/ ++CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags` + LFLAGS = -L../base/ -lm -lpthread + AR_OPTIONS = ru + +@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile +index ef3334a..3a0bc2a 100644 +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm + + + .c.o : +diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile +index 285e6a0..8c6a0dc 100644 +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + make_shotgun : make_shotgun.o shotgun.o + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) +@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm + + + .c.o : +diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile +index d1d77af..cad8900 100644 +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \ + + + +-CC = cc ++CC ?= gcc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` ++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ + LFLAGS = -g -L../base/ -lm + AR_OPTIONS = ru +@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a + $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +diff --git a/src/external/mott/makefile b/src/external/mott/makefile +index 8d7c1d4..940c438 100644 +--- a/src/external/mott/makefile ++++ b/src/external/mott/makefile +@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o + wise2_mott_bridge.o : wise2_mott_bridge.c + $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c + +-CC = cc ++CC ?= gcc + +-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c +-LFLAGS = -g -L../base/ -lm ++CFLAGS += -DPTHREAD -c ++LFLAGS = -L../base/ -lm + AR_OPTIONS = ru + + +diff --git a/src/makefile b/src/makefile +index bdff4ff..0d7c871 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -26,12 +26,12 @@ + + # Change the cc line to gcc if you get compiler errors + # Most likely you have a non ANSI C compiler +-CC ?= cc ++CC ?= gcc + + # These are the CFLAGS to use. These days Wise2 is inherently + # pthreaded, and everything is compiled with threads. More + # info on running threads can be found in the documentation +-CFLAGS = -c -pthread -O2 `glib-config --cflags` ++CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags` + + + +diff --git a/src/models/makefile b/src/models/makefile +index f518d0c..a297eff 100644 +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -50,6 +50,8 @@ NEWG = geneparser21.o \ + proteinsw.o \ + estquick3.o + ++EXTRALIBS += `pkg-config glib-2.0 --libs` ++ + all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a + + libmodel.a : $(NEWG) +@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm ++ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm + + testdna : testdna.o dnaalign.o seqaligndisplay.o + $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) +@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c +@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc. + + + scanwisep_wiseserver.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` + + scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs` + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap. + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread +@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o + $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm ++ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence ++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence ++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +347,11 @@ HMMER_DEFINE = + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` ++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` + #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +diff --git a/src/network/makefile b/src/network/makefile +index 303c2da..e607310 100644 +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags` ++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +diff --git a/src/snp/makefile b/src/snp/makefile +index ccf750a..2b83c43 100644 +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -2,12 +2,12 @@ + .SUFFIXES : .dy + + +-CC = cc ++CC ?= gcc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0 + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch new file mode 100644 index 000000000000..42af0c7e849b --- /dev/null +++ b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch @@ -0,0 +1,302 @@ +diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c +index 5889e7d..bc95629 100644 +--- a/src/HMMer2/sqio.c ++++ b/src/HMMer2/sqio.c +@@ -213,7 +213,7 @@ readline(FILE *f, char *s) + } + } + +-/* Function: getline() ++/* Function: get_line() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ readline(FILE *f, char *s) + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V) + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V) + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V) + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V) + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V) + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V) + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V) + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V) + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V) + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V) + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V) + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V) + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) get_line(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V) + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V) + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V) + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V) + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V) + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V) + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V) + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V) + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V) + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V) + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env) + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset) + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp) + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch new file mode 100644 index 000000000000..827ce4cdfa7a --- /dev/null +++ b/sci-biology/wise/files/wise-api.tex.patch @@ -0,0 +1,38 @@ +--- api.tex.old 2005-03-06 11:31:59.862760952 -0500 ++++ api.tex 2005-03-06 11:42:31.375756384 -0500 +@@ -204,7 +204,7 @@ + \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) + \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins + \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) +-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) ++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) + \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) + \end{itemize} + +@@ -213,7 +213,7 @@ + \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) + \item Make a protein database from the single protein object (\ref{object_ProteinDB}) + \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) +-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) ++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) + \item Show the Hscore object using a show function (\ref{object_Hscore}) + \item Retrieve individual protein objects from the database by taking out the + DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object +@@ -232,7 +232,7 @@ + \item Read in a codon table (\ref{object_CodonTable}) + \item Make a random DNA model (\ref{object_RandomModelDNA}) + \item Make an algorithm type (\ref{module_gwrap}) +-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) ++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) + \item Run the actual algorithm (\ref{module_gwrap}) + \item show the alignment using genedisplay (\ref{module_gwrap}) + \end{itemize} +@@ -5055,7 +5055,7 @@ + Member functions of RandomModel + + \section{sequence\_codon} +-\label{module_sequence\_codon} ++\label{module_sequence_codon} + This module only contains factory methods + + \subsection{sequence\_codon factory methods} diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env new file mode 100644 index 000000000000..3f781c80833b --- /dev/null +++ b/sci-biology/wise/files/wise-env @@ -0,0 +1 @@ +WISECONFIGDIR="/usr/share/wise/wisecfg" diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/wise/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/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild new file mode 100644 index 000000000000..f68686842689 --- /dev/null +++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +DESCRIPTION="Intelligent algorithms for DNA searches" +HOMEPAGE="http://www.ebi.ac.uk/Wise2/" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha amd64 ia64 ~sparc x86" +IUSE="doc static-libs" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND=" + ${RDEPEND} + app-shells/tcsh + dev-lang/perl + virtual/latex-base" + +S="${WORKDIR}"/${PN}$(delete_version_separator 3) + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-glibc-2.10.patch \ + "${FILESDIR}"/${P}-cflags.patch + cd "${S}"/docs || die + cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die + cat wise2api.tex temp.tex apiend.tex > api.tex || die + epatch "${FILESDIR}"/${PN}-api.tex.patch +} + +src_compile() { + emake \ + -C src \ + CC="$(tc-getCC)" \ + all + if use doc; then + cd "${S}"/docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd "${S}"/src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb + use static-libs && \ + dolib.a \ + "${S}"/src/base/libwisebase.a \ + "${S}"/src/dynlibsrc/libdyna.a \ + "${S}"/src/models/libmodel.a + + insinto /usr/share/${PN} + doins -r "${S}"/wisecfg + + if use doc; then + insinto /usr/share/doc/${PF} + doins "${S}"/docs/*.ps + fi + newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" +} |