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10 changed files with 1378 additions and 1 deletions
2
.gitignore
vendored
Normal file
2
.gitignore
vendored
Normal file
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@ -0,0 +1,2 @@
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wise2.2.0.tar.gz
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/wise2.4.1.tar.gz
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@ -1 +0,0 @@
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Orphaned by upstream; no longer needed in Fedora
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1
sources
Normal file
1
sources
Normal file
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@ -0,0 +1 @@
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d70c404c1dc40ceef7718757b11bdaa0 wise2.4.1.tar.gz
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21
wise2-build.patch
Normal file
21
wise2-build.patch
Normal file
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@ -0,0 +1,21 @@
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--- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200
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+++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200
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@@ -109,7 +109,7 @@
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bin :
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mkdir bin
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cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
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- csh welcome.csh
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+ ./welcome.csh
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libs :
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(cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
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diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
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--- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200
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+++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200
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@@ -1,4 +1,4 @@
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-#!/bin/tcsh -f
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+#!/bin/sh
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echo ""
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echo "Welcome to Wise2.4"
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302
wise2-getline.patch
Normal file
302
wise2-getline.patch
Normal file
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@ -0,0 +1,302 @@
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Index: wise-2.4.1/src/HMMer2/sqio.c
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===================================================================
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--- wise-2.4.1.orig/src/HMMer2/sqio.c 2009-10-31 20:10:25.000000000 +0000
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+++ wise-2.4.1/src/HMMer2/sqio.c 2009-10-31 20:11:11.000000000 +0000
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@@ -213,7 +213,7 @@
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}
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}
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-/* Function: getline()
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+/* Function: getline_()
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* Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
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*
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* Purpose: read a line from a sequence file into V->sbuffer.
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@@ -229,7 +229,7 @@
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* Returns: (void)
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*/
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static void
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-getline(struct ReadSeqVars *V)
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+getline_(struct ReadSeqVars *V)
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{
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char *cp;
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@@ -299,7 +299,7 @@
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V->seqlen = 0;
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if (addfirst) addseq(V->sbuffer, V);
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do {
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- getline(V);
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+ getline_(V);
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/* feof() alone is a bug; files not necessarily \n terminated */
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if (*(V->sbuffer) == '\0' && feof(V->f))
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done = TRUE;
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@@ -327,7 +327,7 @@
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char *sptr;
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/* load first line of entry */
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while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
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- getline(V);
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+ getline_(V);
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if (feof(V->f)) return;
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if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
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@@ -336,7 +336,7 @@
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
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}
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do {
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- getline(V);
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+ getline_(V);
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if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
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SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
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else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
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@@ -345,7 +345,7 @@
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
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}
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} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
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- getline(V); /* skip next line, coords */
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+ getline_(V); /* skip next line, coords */
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readLoop(0, endPIR, V);
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@@ -359,7 +359,7 @@
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/* get next line
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*/
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while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
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- getline(V);
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+ getline_(V);
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}
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@@ -377,7 +377,7 @@
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char *nm;
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/* position past ';' comments */
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do {
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- getline(V);
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+ getline_(V);
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} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
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if (!feof(V->f))
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@@ -389,7 +389,7 @@
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}
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while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
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- getline(V);
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+ getline_(V);
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}
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static int
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@@ -411,7 +411,7 @@
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if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
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}
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- getline(V);
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+ getline_(V);
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}
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if (! feof(V->f))
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@@ -420,7 +420,7 @@
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/* load next line
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*/
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while ((!feof(V->f)) && (*V->sbuffer != ';'))
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- getline(V);
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+ getline_(V);
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}
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@@ -438,7 +438,7 @@
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int in_definition;
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while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
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- getline(V);
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+ getline_(V);
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if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
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{
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@@ -449,7 +449,7 @@
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in_definition = FALSE;
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while (! feof(V->f))
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{
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- getline(V);
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+ getline_(V);
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if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
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{
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if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
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@@ -482,11 +482,11 @@
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while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
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- getline(V);
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+ getline_(V);
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/* SRE: V->s now holds "//", so sequential
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reads are wedged: fixed Tue Jul 13 1993 */
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while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
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- getline(V);
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+ getline_(V);
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}
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static int
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@@ -515,7 +515,7 @@
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Die("bogus GCGdata format? %s", V->sbuffer);
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/* second line contains free text description */
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- getline(V);
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+ getline_(V);
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SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
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if (binary) {
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@@ -535,7 +535,7 @@
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else readLoop(0, endGCGdata, V);
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while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
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- getline(V);
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+ getline_(V);
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}
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static int
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@@ -555,12 +555,12 @@
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if ((sptr = strtok(NULL, "\n")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
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/* workaround for long NCBI NR lines */
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- while (V->longline && ! feof(V->f)) getline(V);
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+ while (V->longline && ! feof(V->f)) getline_(V);
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readLoop(0, endPearson, V);
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while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
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- getline(V);
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+ getline_(V);
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}
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@@ -587,7 +587,7 @@
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/* make sure we have first line */
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while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
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- getline(V);
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+ getline_(V);
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if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
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{
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@@ -596,7 +596,7 @@
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}
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do {
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- getline(V);
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+ getline_(V);
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if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
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{
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if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
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@@ -620,7 +620,7 @@
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/* load next record's ID line */
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while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
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- getline(V);
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+ getline_(V);
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}
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@@ -636,7 +636,7 @@
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{
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char *sptr;
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- getline(V); /*s == "seqLen seqid string..."*/
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+ getline_(V); /*s == "seqLen seqid string..."*/
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if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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@@ -647,7 +647,7 @@
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readLoop(0, endZuker, V);
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while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
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- getline(V);
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+ getline_(V);
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}
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static void
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@@ -669,7 +669,7 @@
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do {
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done = feof(V->f);
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- getline(V);
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+ getline_(V);
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if (! done) addseq(V->sbuffer, V);
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} while (!done);
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}
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@@ -681,7 +681,7 @@
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char *sptr;
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int dostruc = FALSE;
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- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
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+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V);
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if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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@@ -689,7 +689,7 @@
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/*CONSTCOND*/
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while (1)
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{
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- getline(V);
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+ getline_(V);
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if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
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if (strncmp(V->sbuffer, "SRC ", 4) == 0)
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@@ -721,14 +721,14 @@
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while (1)
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{
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/* sequence line */
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- getline(V);
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+ getline_(V);
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if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
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break;
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addseq(V->sbuffer, V);
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/* structure line */
|
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if (dostruc)
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{
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- getline(V);
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+ getline_(V);
|
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if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
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addstruc(V->sbuffer, V);
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}
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@@ -736,7 +736,7 @@
|
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while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
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- getline(V);
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+ getline_(V);
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}
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@@ -816,7 +816,7 @@
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/* Load the first line.
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*/
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- getline(dbfp);
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+ getline_(dbfp);
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return dbfp;
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}
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@@ -833,7 +833,7 @@
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Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
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fseek(sqfp->f, offset, SEEK_SET);
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- getline(sqfp);
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+ getline_(sqfp);
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}
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@@ -853,7 +853,7 @@
|
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if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
|
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else {
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rewind(sqfp->f);
|
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- getline(sqfp);
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+ getline_(sqfp);
|
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}
|
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}
|
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@@ -949,7 +949,7 @@
|
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do { /* skip leading comments on GCG file */
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gotuw = (strstr(V->sbuffer,"..") != NULL);
|
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if (gotuw) readUWGCG(V);
|
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- getline(V);
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+ getline_(V);
|
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} while (! feof(V->f));
|
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break;
|
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703
wise2-glib2.patch
Normal file
703
wise2-glib2.patch
Normal file
|
|
@ -0,0 +1,703 @@
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|||
Author: Barry deFreese <bdefreese@debian.org>
|
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Description: To build wise2 with the Glib version 2.0 instead of 1.2.
|
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Forwarded: birney@sanger.ac.uk
|
||||
--- a/src/makefile
|
||||
+++ b/src/makefile
|
||||
@@ -31,13 +31,13 @@
|
||||
|
||||
|
||||
# Intel icc flags
|
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-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags`
|
||||
+# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0`
|
||||
|
||||
# alpha flags (-pthread)
|
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-# CFLAGS = -c -O3 -pthread `glib-config --cflags`
|
||||
+# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0`
|
||||
|
||||
# normal linux/bsd/mac flags
|
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-CFLAGS = -c -O3 `glib-config --cflags`
|
||||
+CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0`
|
||||
|
||||
|
||||
EXTRALIBS = -lm
|
||||
--- a/src/snp/makefile
|
||||
+++ b/src/snp/makefile
|
||||
@@ -5,9 +5,9 @@
|
||||
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 += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
|
||||
|
||||
-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
|
||||
+LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm
|
||||
AR_OPTIONS = ru
|
||||
|
||||
RANLIB_NEEDED = 0
|
||||
@@ -16,7 +16,7 @@
|
||||
$(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) -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 $(LDFLAGS)
|
||||
|
||||
INCFLAGS = -I../base/ -I../dynlibsrc/
|
||||
DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
|
||||
--- a/src/corba/makefile
|
||||
+++ b/src/corba/makefile
|
||||
@@ -3,9 +3,9 @@
|
||||
CC = cc
|
||||
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`
|
||||
-LFLAGS = -L../base/ -lm -lpthread
|
||||
+#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
|
||||
+CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
|
||||
+LDFLAGS += -L../base/ -lm -lpthread
|
||||
AR_OPTIONS = ru
|
||||
|
||||
|
||||
@@ -14,18 +14,18 @@
|
||||
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 -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 `pkg-config --libs glib-2.0` -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 -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 --libs glib-2.0` -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 -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -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 -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 `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
|
||||
|
||||
.c.o :
|
||||
$(CC) $(CFLAGS) $(INCFLAGS) $?
|
||||
--- a/src/models/makefile
|
||||
+++ b/src/models/makefile
|
||||
@@ -62,46 +62,46 @@
|
||||
# $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c
|
||||
|
||||
testgenestat : testgenestat.o genestats.o pwmdna.o
|
||||
- $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_aligng : test_aligng.o aligngenemodel.o pwmdna.o
|
||||
- $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
makepwm : makepwm.o pwmdna.o
|
||||
- $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
testwise2xhmmer2.o : testwise2xhmmer2.c
|
||||
$(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c
|
||||
|
||||
testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o
|
||||
- $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS)
|
||||
+ $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS)
|
||||
|
||||
plan7test.o : plan7test.c
|
||||
$(CC) $(CFLAGS) -I../HMMer2/ plan7test.c
|
||||
|
||||
plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o
|
||||
- $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS)
|
||||
+ $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS)
|
||||
|
||||
seqstat : seqstat.o
|
||||
- $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
mutatedna : mutatedna.o
|
||||
- $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
revcomp : revcomp.o
|
||||
- $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
stupid_motif_scan : stupid_motif_scan.o
|
||||
- $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
seqtrunc : seqtrunc.o
|
||||
- $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
seqlist : seqlist.o
|
||||
- $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
testpwm : testpwm.o pwmdna.o
|
||||
- $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence
|
||||
+ $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence
|
||||
|
||||
|
||||
threestate : $(MODELOBJ)
|
||||
@@ -111,29 +111,29 @@
|
||||
pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o
|
||||
|
||||
test : test.o proteinsw.o protprotdis.o
|
||||
- $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS)
|
||||
+ $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS)
|
||||
|
||||
testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o
|
||||
- $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
test_tf : test_transfactor.o transfactor.o pwmdna.o
|
||||
- $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o
|
||||
- $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o
|
||||
- $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o
|
||||
- $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
|
||||
cdtest : cdtest.o cdna2genomic.o d2d_display.o
|
||||
- $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
prob2bits : prob2bits.o
|
||||
- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase
|
||||
+ $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase
|
||||
|
||||
quick :
|
||||
cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c
|
||||
@@ -180,161 +180,161 @@
|
||||
$(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
|
||||
+ $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase
|
||||
|
||||
testdna : testdna.o dnaalign.o seqaligndisplay.o
|
||||
- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
dnal : dnal.o dnaalign.o seqaligndisplay.o
|
||||
- $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
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 $(EXTRALIBS)
|
||||
+ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
scanwisep.o : scanwisep.c
|
||||
- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
|
||||
+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $?
|
||||
|
||||
hsp2aln_sw.o : hsp2aln_sw.c
|
||||
- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
|
||||
+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
|
||||
|
||||
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
|
||||
|
||||
scanwisep_mysql : scanwisep_mysql.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 ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ
|
||||
+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ
|
||||
|
||||
|
||||
scanwisep_corba.o : scanwisep.c
|
||||
$(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c
|
||||
|
||||
scanwisep_corba : scanwisep_corba.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 ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread
|
||||
+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread
|
||||
|
||||
|
||||
scanwisep_wiseserver.o : scanwisep.c
|
||||
$(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
|
||||
|
||||
scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
|
||||
- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
|
||||
+ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
|
||||
|
||||
scanwisep_compress.o : scanwisep.c
|
||||
$(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
|
||||
|
||||
scanwisep_compress : scanwisep_compress.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 ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
|
||||
+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
|
||||
|
||||
|
||||
|
||||
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 $(EXTRALIBS) `glib-config --libs` -lpthread
|
||||
+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(EXTRALIBS) `glib-config --libs` -lpthread
|
||||
+ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
|
||||
|
||||
localcishit.o : localcishit.c
|
||||
- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
|
||||
+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
|
||||
|
||||
promoterwise.o : promoterwise.c
|
||||
- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
|
||||
+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
|
||||
|
||||
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 $(EXTRALIBS) `glib-config --libs` -lpthread
|
||||
+ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 -lpthread
|
||||
+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread
|
||||
|
||||
pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
|
||||
- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
|
||||
- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS)
|
||||
+ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS)
|
||||
|
||||
dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o
|
||||
- $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
lba : lba.o largeblockdp.o seqaligndisplay.o
|
||||
- $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
|
||||
fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o
|
||||
- $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o
|
||||
- $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o
|
||||
- $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
makerandomdb : makerandomdb.o
|
||||
- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
genewise : genewise.o $(NEWG)
|
||||
- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
cdnawise : cdnawise.o $(NEWG) cdnawise10.o
|
||||
- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(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
|
||||
+ $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase
|
||||
|
||||
|
||||
efgw : genewise.o $(NEWG)
|
||||
- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
|
||||
+ $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
|
||||
|
||||
|
||||
genewisedb : genewisedb.o $(NEWG)
|
||||
- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
estwisedb : estwisedb.o $(NEWG)
|
||||
- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
edb : estwisedb.o $(NEWG)
|
||||
- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
|
||||
+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
|
||||
|
||||
estwise : estwise.o $(NEWG)
|
||||
- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
|
||||
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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
pseudowise : pseudowise.o pseudowise7.o $(NEWG)
|
||||
- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
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 $(EXTRALIBS)
|
||||
+ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
|
||||
HMMER_LIBS = ../HMMer2/
|
||||
@@ -345,11 +345,11 @@
|
||||
CC = cc
|
||||
#CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
|
||||
#CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
|
||||
-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
|
||||
-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
|
||||
-#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
|
||||
+CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
|
||||
+#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
|
||||
+#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
|
||||
|
||||
-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
|
||||
+LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0`
|
||||
AR_OPTIONS = ru
|
||||
|
||||
RANLIB_NEEDED = 0
|
||||
@@ -360,7 +360,7 @@
|
||||
|
||||
|
||||
#test : test.o libwisedb.a
|
||||
-# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS)
|
||||
+# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS)
|
||||
|
||||
|
||||
#
|
||||
--- a/src/dnaindex/makefile
|
||||
+++ b/src/dnaindex/makefile
|
||||
@@ -27,53 +27,53 @@
|
||||
|
||||
|
||||
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 $(LDFLAGS) `pkg-config --libs glib-2.0`
|
||||
|
||||
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 $(LDFLAGS) `pkg-config --libs glib-2.0`
|
||||
|
||||
|
||||
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 $(LDFLAGS) `pkg-config --libs glib-2.0`
|
||||
|
||||
make_shotgun : make_shotgun.o shotgun.o
|
||||
- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_dnanumber : test_dnanumber.o dnanumber.o
|
||||
- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_linkindex : test_linkindex.o linkindex.o dnanumber.o
|
||||
- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_forwardindex : test_forwardindex.o forwardindex.o
|
||||
- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_euler : test_euler.o eulerindex.o singleseqspace.o
|
||||
- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o
|
||||
- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o
|
||||
- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o
|
||||
- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o
|
||||
- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
show_euler : show_euler.o eulerindex.o singleseqspace.o
|
||||
- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
|
||||
+ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS)
|
||||
|
||||
CC = cc
|
||||
-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
|
||||
+CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
|
||||
|
||||
|
||||
-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
|
||||
+LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
|
||||
|
||||
|
||||
.c.o :
|
||||
--- a/src/dnaindex/assembly/makefile
|
||||
+++ b/src/dnaindex/assembly/makefile
|
||||
@@ -3,33 +3,33 @@
|
||||
.SUFFIXES : .dy
|
||||
|
||||
test_basegraph : test_basegraph.o basegraph.o
|
||||
- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o
|
||||
- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
|
||||
test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o
|
||||
- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
|
||||
pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o
|
||||
- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
|
||||
badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o
|
||||
- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
|
||||
- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase
|
||||
+ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase
|
||||
|
||||
|
||||
|
||||
CC = cc
|
||||
-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
|
||||
+CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0`
|
||||
|
||||
|
||||
-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
|
||||
+LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
|
||||
|
||||
|
||||
.c.o :
|
||||
--- a/src/dynlibsrc/makefile
|
||||
+++ b/src/dynlibsrc/makefile
|
||||
@@ -84,11 +84,11 @@
|
||||
CC = cc
|
||||
INCFLAGS = -I../base/
|
||||
#CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
|
||||
-CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags`
|
||||
-#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags`
|
||||
-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags`
|
||||
+CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
|
||||
+#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
|
||||
+#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
|
||||
#CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
|
||||
-LFLAGS = -g -L../base/ -lm
|
||||
+LDFLAGS += -g -L../base/ -lm
|
||||
AR_OPTIONS = ru
|
||||
|
||||
RANLIB_NEEDED = 0
|
||||
@@ -133,47 +133,47 @@
|
||||
#
|
||||
|
||||
test_genomic : genomic.o test_genomic.o sequence.o codon.o
|
||||
- $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm
|
||||
|
||||
test_tree : tree.o test_tree.o
|
||||
- $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm
|
||||
|
||||
test_intallocator : intallocator.o test_intallocator.o
|
||||
- $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm
|
||||
|
||||
test_psi : test_psi.o proteinstreamedindex.o
|
||||
- $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm
|
||||
|
||||
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
|
||||
+ $(CC) $(LDFLAGS) -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) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` 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) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
|
||||
|
||||
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) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
|
||||
|
||||
|
||||
testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
|
||||
- $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
|
||||
|
||||
testseqalign : seqalign.o testseqalign.o sequence.o codon.o
|
||||
- $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm
|
||||
|
||||
testanc : libdyna.a
|
||||
- $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm
|
||||
|
||||
testdb : testdb.o sequencedb.o sequence.o codon.o probability.o
|
||||
- $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm
|
||||
|
||||
testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o
|
||||
- $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm
|
||||
|
||||
testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o
|
||||
- $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
|
||||
+ $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
|
||||
|
||||
.c.o :
|
||||
$(CC) $(CFLAGS) $(INCFLAGS) $?
|
||||
--- 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 -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 += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0`
|
||||
+LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0`
|
||||
AR_OPTIONS = ru
|
||||
|
||||
RANLIB_NEEDED = 0
|
||||
@@ -13,7 +13,7 @@
|
||||
|
||||
|
||||
scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o
|
||||
- $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread
|
||||
+ $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread
|
||||
|
||||
|
||||
.c.o :
|
||||
--- a/src/other_programs/makefile
|
||||
+++ b/src/other_programs/makefile
|
||||
@@ -3,8 +3,8 @@
|
||||
.SUFFIXES : .dy
|
||||
|
||||
CC = cc
|
||||
-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags`
|
||||
-LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs`
|
||||
+CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0`
|
||||
+LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0`
|
||||
AR_OPTIONS = ru
|
||||
|
||||
RANLIB_NEEDED = 0
|
||||
--- a/src/base/makefile
|
||||
+++ b/src/base/makefile
|
||||
@@ -19,9 +19,9 @@
|
||||
|
||||
|
||||
|
||||
-#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH
|
||||
-CFLAGS = -c -O2 -DUNIX -pthread
|
||||
-LFLAGS = -g -lm
|
||||
+#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH
|
||||
+CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread
|
||||
+LDFLAGS += -g -lm
|
||||
DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
|
||||
AR_OPTIONS = ru
|
||||
|
||||
--- a/src/HMMer2/Makefile
|
||||
+++ b/src/HMMer2/Makefile
|
||||
@@ -13,7 +13,7 @@
|
||||
## your compiler and compiler flags
|
||||
#
|
||||
CC = cc
|
||||
-CFLAGS = -g
|
||||
+CFLAGS += $(CPPFLAGS) -g
|
||||
|
||||
## machine specific definitions
|
||||
#
|
||||
@@ -75,25 +75,25 @@
|
||||
all: $(PROGS)
|
||||
|
||||
hmmalign: $(OBJ) hmmalign.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS)
|
||||
|
||||
hmmbuild: $(OBJ) hmmbuild.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS)
|
||||
|
||||
hmmcalibrate: $(OBJ) hmmcalibrate.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS)
|
||||
|
||||
hmmconvert: $(OBJ) hmmconvert.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS)
|
||||
|
||||
hmmemit: $(OBJ) hmmemit.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS)
|
||||
|
||||
hmmpfam: $(OBJ) hmmpfam.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS)
|
||||
|
||||
hmmsearch: $(OBJ) hmmsearch.o
|
||||
- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS)
|
||||
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS)
|
||||
|
||||
#######
|
||||
## Target used in making Shiva test suite
|
||||
18
wise2-isnumber.patch
Executable file
18
wise2-isnumber.patch
Executable file
|
|
@ -0,0 +1,18 @@
|
|||
#! /bin/sh /usr/share/dpatch/dpatch-run
|
||||
## 02_isnumber.dpatch by Philipp Benner <mail@philipp-benner.de>
|
||||
##
|
||||
## DP: Replace isnumber() (which does not exist on linux) by isdigit().
|
||||
|
||||
@DPATCH@
|
||||
diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
|
||||
--- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200
|
||||
+++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200
|
||||
@@ -20,7 +20,7 @@
|
||||
if( line[0] == '#' ) {
|
||||
continue;
|
||||
}
|
||||
- if( !isnumber(line[0]) ) {
|
||||
+ if( !isdigit(line[0]) ) {
|
||||
warn("Bad looking line in intron file, %s",line);
|
||||
continue;
|
||||
}
|
||||
54
wise2-ld--as-needed.patch
Normal file
54
wise2-ld--as-needed.patch
Normal file
|
|
@ -0,0 +1,54 @@
|
|||
Description: Fix FTBFS with ld --as-needed.
|
||||
Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
|
||||
|
||||
diff --git a/src/models/makefile b/src/models/makefile
|
||||
index 1766fee..e4634b5 100644
|
||||
--- a/src/models/makefile
|
||||
+++ b/src/models/makefile
|
||||
@@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c
|
||||
$(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
|
||||
|
||||
scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
|
||||
- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
|
||||
+ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS)
|
||||
|
||||
scanwisep_compress.o : scanwisep.c
|
||||
$(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
|
||||
@@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o
|
||||
$(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
genewise : genewise.o $(NEWG)
|
||||
- $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS)
|
||||
|
||||
cdnawise : cdnawise.o $(NEWG) cdnawise10.o
|
||||
$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
@@ -300,16 +300,16 @@ efgw : genewise.o $(NEWG)
|
||||
|
||||
|
||||
genewisedb : genewisedb.o $(NEWG)
|
||||
- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS)
|
||||
|
||||
estwisedb : estwisedb.o $(NEWG)
|
||||
- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS)
|
||||
|
||||
edb : estwisedb.o $(NEWG)
|
||||
$(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
|
||||
|
||||
estwise : estwise.o $(NEWG)
|
||||
- $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS)
|
||||
|
||||
|
||||
amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o
|
||||
@@ -331,7 +331,7 @@ 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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
|
||||
pseudowise : pseudowise.o pseudowise7.o $(NEWG)
|
||||
- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
+ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS)
|
||||
|
||||
clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
|
||||
$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
|
||||
99
wise2-mayhem.patch
Normal file
99
wise2-mayhem.patch
Normal file
|
|
@ -0,0 +1,99 @@
|
|||
--- a/src/models/dbac.c
|
||||
+++ b/src/models/dbac.c
|
||||
@@ -535,8 +535,12 @@
|
||||
*
|
||||
*/
|
||||
|
||||
- one = read_fasta_file_Sequence(*argv++);
|
||||
- two = read_fasta_file_Sequence(*argv++);
|
||||
+ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) {
|
||||
+ fatal("Unable to read the sequence in file");
|
||||
+ }
|
||||
+ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) {
|
||||
+ fatal("Unable to read the sequence in file");
|
||||
+ }
|
||||
|
||||
uppercase_Sequence(one);
|
||||
uppercase_Sequence(two);
|
||||
--- a/src/models/estwise.c
|
||||
+++ b/src/models/estwise.c
|
||||
@@ -313,7 +313,7 @@
|
||||
}
|
||||
}
|
||||
|
||||
- if( reverse == TRUE ) {
|
||||
+ if( cdna && reverse == TRUE ) {
|
||||
if( tstart > tend ) {
|
||||
warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
|
||||
}
|
||||
@@ -323,7 +323,7 @@
|
||||
cdna = cdna_temp;
|
||||
}
|
||||
|
||||
- if( target_abs == TRUE ) {
|
||||
+ if( cdna && target_abs == TRUE ) {
|
||||
cdna->baseseq->offset = 1;
|
||||
cdna->baseseq->end = strlen(cdna->baseseq->seq);
|
||||
}
|
||||
@@ -472,8 +472,11 @@
|
||||
}
|
||||
|
||||
cp = flat_cDNAParser(indel_error);
|
||||
- cm = flat_CodonMapper(ct);
|
||||
- sprinkle_errors_over_CodonMapper(cm,subs_error);
|
||||
+
|
||||
+ if( ct ) {
|
||||
+ cm = flat_CodonMapper(ct);
|
||||
+ sprinkle_errors_over_CodonMapper(cm,subs_error);
|
||||
+ }
|
||||
|
||||
return ret;
|
||||
|
||||
--- a/src/models/genewise.c
|
||||
+++ b/src/models/genewise.c
|
||||
@@ -550,8 +550,10 @@
|
||||
ret = FALSE;
|
||||
}
|
||||
|
||||
- gen->baseseq->offset = 1;
|
||||
- gen->baseseq->end = strlen(gen->baseseq->seq);
|
||||
+ if ( gen ) {
|
||||
+ gen->baseseq->offset = 1;
|
||||
+ gen->baseseq->end = strlen(gen->baseseq->seq);
|
||||
+ }
|
||||
}
|
||||
|
||||
if( alg_str != NULL ) {
|
||||
--- a/src/models/estwisedb.c
|
||||
+++ b/src/models/estwisedb.c
|
||||
@@ -688,8 +688,11 @@
|
||||
|
||||
|
||||
cps = flat_cDNAParser(indel_error);
|
||||
- cm = flat_CodonMapper(ct);
|
||||
- sprinkle_errors_over_CodonMapper(cm,subs_error);
|
||||
+
|
||||
+ if( ct ) {
|
||||
+ cm = flat_CodonMapper(ct);
|
||||
+ sprinkle_errors_over_CodonMapper(cm,subs_error);
|
||||
+ }
|
||||
|
||||
return ret;
|
||||
|
||||
--- a/src/models/promoterwise.c
|
||||
+++ b/src/models/promoterwise.c
|
||||
@@ -147,8 +147,12 @@
|
||||
|
||||
lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
|
||||
|
||||
- query = read_fasta_file_Sequence(argv[1]);
|
||||
- target = read_fasta_file_Sequence(argv[2]);
|
||||
+ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) {
|
||||
+ fatal("Unable to read the sequence in query file");
|
||||
+ }
|
||||
+ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) {
|
||||
+ fatal("Unable to read the sequence in target file");
|
||||
+ }
|
||||
|
||||
for(i=0;i<query->len;i++) {
|
||||
query->seq[i] = toupper(query->seq[i]);
|
||||
178
wise2.spec
Normal file
178
wise2.spec
Normal file
|
|
@ -0,0 +1,178 @@
|
|||
%if 0%{?epel} < 7
|
||||
%{!?__global_ldflags: %global __global_ldflags -Wl,-z,relro}
|
||||
%endif
|
||||
|
||||
Name: wise2
|
||||
Version: 2.4.1
|
||||
Release: 1%{?dist}
|
||||
Summary: Tools for comparison of bio-polymers
|
||||
|
||||
Group: Applications/Engineering
|
||||
## Everything is licensed under a BSD-style license except for
|
||||
## the HMMer2 libraries and models directory which are GPLv2+
|
||||
## see LICENSE files for details.
|
||||
License: BSD and GPLv2+
|
||||
URL: http://www.ebi.ac.uk/~birney/%{name}/
|
||||
Source0: http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz
|
||||
|
||||
## Patches from Debian package. Thanks to Philipp Benner
|
||||
Patch0: %{name}-build.patch
|
||||
Patch1: %{name}-isnumber.patch
|
||||
Patch2: %{name}-glib2.patch
|
||||
Patch3: %{name}-getline.patch
|
||||
Patch4: %{name}-ld--as-needed.patch
|
||||
Patch5: %{name}-mayhem.patch
|
||||
|
||||
BuildRequires: glib2-devel
|
||||
BuildRequires: strace
|
||||
BuildRequires: pkgconfig
|
||||
|
||||
%description
|
||||
Wise2 is a package focused on comparisons of bio-polymers, commonly DNA
|
||||
sequence and protein sequence. A strength of Wise2 is the
|
||||
comparison of DNA sequence at the level of its protein
|
||||
translation. This comparison allows the simultaneous prediction of
|
||||
gene structure with homology based alignment.
|
||||
|
||||
%package doc
|
||||
Summary: Wise2 documentation
|
||||
Group: Development/Libraries
|
||||
BuildArch: noarch
|
||||
%description doc
|
||||
Wise2, Wise2api and Dynamite documentation files.
|
||||
|
||||
%package examples
|
||||
Summary: Wise2 examples
|
||||
Group: Development/Libraries
|
||||
Requires: %{name}%{?_isa} = %{version}-%{release}
|
||||
%description examples
|
||||
Here are some examples that you might want to try out. The
|
||||
Wise2 executables of course should be installed before.
|
||||
|
||||
%prep
|
||||
%setup -q -n wise%{version}
|
||||
%patch0 -p1
|
||||
%patch1 -p1
|
||||
%patch2 -p1
|
||||
%patch3 -p1
|
||||
%patch4 -p1
|
||||
|
||||
# Remove spurious-executable-perm
|
||||
chmod a-x src/external/mott/mott_api.c
|
||||
chmod a-x src/external/mott/mott_api.h
|
||||
chmod a-x src/external/mott/gaplib.c
|
||||
chmod a-x src/external/mott/gapstat.h
|
||||
|
||||
## fix interpreter in examples
|
||||
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl
|
||||
## fix perms
|
||||
chmod -x test_data/rrm.HMM
|
||||
|
||||
## pull out licenses
|
||||
for i in base dynlibsrc dyc
|
||||
do
|
||||
cp src/$i/LICENSE LICENSE.$i
|
||||
done
|
||||
cp src/models/GNULICENSE LICENSE.GPL
|
||||
|
||||
%build
|
||||
## removed "{?_smp_mflags}", does not support parallel build
|
||||
export LDFLAGS="%{__global_ldflags}"
|
||||
make -C src CC=gcc \
|
||||
CFLAGS=" -c $RPM_OPT_FLAGS -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all
|
||||
|
||||
%install
|
||||
pushd src/bin
|
||||
mkdir -p $RPM_BUILD_ROOT%{_bindir}
|
||||
for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb
|
||||
do
|
||||
install -pm 755 $i $RPM_BUILD_ROOT%{_bindir}
|
||||
done
|
||||
popd
|
||||
|
||||
# install architecture-independent data and config files
|
||||
mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2
|
||||
pushd wisecfg
|
||||
install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2
|
||||
popd
|
||||
|
||||
# install architecture-independent files to run example tests
|
||||
mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples
|
||||
pushd test_data
|
||||
install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples
|
||||
popd
|
||||
|
||||
# install scripts to automatically set the WISECONFIGDIR environment variable
|
||||
mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d
|
||||
echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh
|
||||
echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh
|
||||
|
||||
%check
|
||||
export WISECONFIGDIR=$PWD/wisecfg
|
||||
make -C src test
|
||||
|
||||
%files
|
||||
%doc README
|
||||
%license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL
|
||||
%{_bindir}/genewisedb
|
||||
%{_bindir}/estwisedb
|
||||
%{_bindir}/genewise
|
||||
%{_bindir}/estwise
|
||||
%{_bindir}/scanwise
|
||||
%{_bindir}/promoterwise
|
||||
%{_bindir}/pswdb
|
||||
%{_bindir}/dba
|
||||
%{_bindir}/psw
|
||||
%{_bindir}/scanwise_server
|
||||
%{_bindir}/dnal
|
||||
%{_datadir}/wise2/
|
||||
%config(noreplace) %{_sysconfdir}/profile.d/*
|
||||
|
||||
%files doc
|
||||
%license LICENSE
|
||||
%doc docs
|
||||
|
||||
%files examples
|
||||
%doc test_data/README
|
||||
%{_datadir}/wise2/examples/
|
||||
|
||||
%changelog
|
||||
* Tue May 05 2015 Antonio Trande <sagitterATfedoraproject.org> - 2.4.1-1
|
||||
- Update to 2.4.1
|
||||
- Fix compiler flags
|
||||
|
||||
* Sun Aug 04 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-12
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
|
||||
|
||||
* Fri Feb 15 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-11
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
|
||||
|
||||
* Sun Jul 22 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-10
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
|
||||
|
||||
* Sat Jan 14 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-9
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
|
||||
|
||||
* Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-8
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
|
||||
|
||||
* Mon Jul 27 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-7
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
|
||||
|
||||
* Thu Jul 16 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-6
|
||||
- Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627)
|
||||
|
||||
* Wed Feb 25 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-5
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
|
||||
|
||||
* Sat Feb 9 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-4
|
||||
- rebuilt for GCC 4.3 as requested by Fedora Release Engineering
|
||||
|
||||
* Thu Aug 16 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-3
|
||||
- Clarify license as BSD and GPLv2+
|
||||
|
||||
* Thu Apr 12 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-2
|
||||
- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius.
|
||||
|
||||
* Wed Apr 11 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-1
|
||||
- Initial Fedora package.
|
||||
Loading…
Add table
Add a link
Reference in a new issue