diff --git a/EMBOSS-6.6.0-fix-conflict-with-pscan.patch b/EMBOSS-6.6.0-fix-conflict-with-pscan.patch new file mode 100644 index 0000000..93a439b --- /dev/null +++ b/EMBOSS-6.6.0-fix-conflict-with-pscan.patch @@ -0,0 +1,695 @@ +diff -up EMBOSS-6.6.0/emboss/acd/epscan.acd.fixconflict EMBOSS-6.6.0/emboss/acd/epscan.acd +--- EMBOSS-6.6.0/emboss/acd/epscan.acd.fixconflict 2015-10-30 09:50:32.562390934 -0400 ++++ EMBOSS-6.6.0/emboss/acd/epscan.acd 2015-10-30 09:50:32.562390934 -0400 +@@ -0,0 +1,63 @@ ++application: epscan [ ++ documentation: "Scans protein sequence(s) with fingerprints from ++ the PRINTS database" ++ groups: "Protein:Motifs" ++ relations: "EDAM:0000158 topic Sequence motifs" ++ relations: "EDAM:0000382 operation Sequence motif recognition (protein)" ++ relations: "EDAM:0000347 operation Sequence database search ++ (by motif or pattern)" ++ relations: "EDAM:0000340 operation Protein secondary database search" ++] ++ ++section: input [ ++ information: "Input section" ++ type: "page" ++] ++ ++ seqall: sequence [ ++ parameter: "Y" ++ type: "Protein" ++ relations: "EDAM:0002886 data Sequence record (protein)" ++ ] ++ ++endsection: input ++ ++section: required [ ++ information: "Required section" ++ type: "page" ++] ++ ++ integer: emin [ ++ standard: "Y" ++ minimum: "1" ++ maximum: "20" ++ default: "2" ++ information: "Minimum number of elements per fingerprint" ++ relations: "EDAM:0002527 data Parameter or primitive" ++ ] ++ ++ integer: emax [ ++ standard: "Y" ++ minimum: "$(emin)" ++ maximum: "20" ++ failrange: "N" ++ trueminimum: "N" ++ default: "20" ++ information: "Maximum number of elements per fingerprint" ++ relations: "EDAM:0002527 data Parameter or primitive" ++ ] ++ ++endsection: required ++ ++section: output [ ++ information: "Output section" ++ type: "page" ++] ++ ++ outfile: outfile [ ++ parameter: "Y" ++ knowntype: "pscan output" ++ relations: "EDAM:0001420 data Sequence-profile alignment (fingerprint)" ++ ] ++ ++endsection: output +diff -up EMBOSS-6.6.0/emboss/acd/Makefile.am.fixconflict EMBOSS-6.6.0/emboss/acd/Makefile.am +--- EMBOSS-6.6.0/emboss/acd/Makefile.am.fixconflict 2013-07-15 17:25:46.000000000 -0400 ++++ EMBOSS-6.6.0/emboss/acd/Makefile.am 2015-10-30 09:50:32.562390934 -0400 +@@ -264,7 +264,7 @@ profit.acd \ + prophecy.acd \ + prophet.acd \ + prosextract.acd \ +-pscan.acd \ ++epscan.acd \ + psiphi.acd \ + rebaseextract.acd \ + recoder.acd \ +diff -up EMBOSS-6.6.0/emboss/acd/Makefile.in.fixconflict EMBOSS-6.6.0/emboss/acd/Makefile.in +--- EMBOSS-6.6.0/emboss/acd/Makefile.in.fixconflict 2013-07-15 17:27:30.000000000 -0400 ++++ EMBOSS-6.6.0/emboss/acd/Makefile.in 2015-10-30 09:50:32.562390934 -0400 +@@ -532,7 +532,7 @@ profit.acd \ + prophecy.acd \ + prophet.acd \ + prosextract.acd \ +-pscan.acd \ ++epscan.acd \ + psiphi.acd \ + rebaseextract.acd \ + recoder.acd \ +diff -up EMBOSS-6.6.0/emboss/acd/printsextract.acd.fixconflict EMBOSS-6.6.0/emboss/acd/printsextract.acd +--- EMBOSS-6.6.0/emboss/acd/printsextract.acd.fixconflict 2012-03-12 13:46:17.000000000 -0400 ++++ EMBOSS-6.6.0/emboss/acd/printsextract.acd 2015-10-30 09:50:32.562390934 -0400 +@@ -1,5 +1,5 @@ + application: printsextract [ +- documentation: "Extract data from PRINTS database for use by pscan" ++ documentation: "Extract data from PRINTS database for use by epscan" + groups: "Utils:Database creation" + gui: "no" + batch: "no" +diff -up EMBOSS-6.6.0/emboss/data/edamtoacd.dat.fixconflict EMBOSS-6.6.0/emboss/data/edamtoacd.dat +--- EMBOSS-6.6.0/emboss/data/edamtoacd.dat.fixconflict 2009-09-30 12:53:21.000000000 -0400 ++++ EMBOSS-6.6.0/emboss/data/edamtoacd.dat 2015-10-30 09:50:32.563390927 -0400 +@@ -159,7 +159,7 @@ outfile | "EDAM:Primer report" + outfile | "EDAM:Primer report" | knowntype:"primersearch output" + outfile | "EDAM:Sequence-profile alignment report" | knowntype:"profit output" + outfile | "EDAM:Sequence profile record" | knowntype:"prophecy output" +-outfile | "EDAM:Fingerprint alignment report" | knowntype:"pscan output" ++outfile | "EDAM:Fingerprint alignment report" | knowntype:"epscan output" + outfile | "EDAM:Restriction enzyme report" | knowntype:"redata output" + outfile | "EDAM:Restriction map report" | knowntype:"remap output" + outfile | "EDAM:EMBOSS restover recognition site report" | knowntype:"restover output" +diff -up EMBOSS-6.6.0/emboss/epscan.c.fixconflict EMBOSS-6.6.0/emboss/epscan.c +--- EMBOSS-6.6.0/emboss/epscan.c.fixconflict 2015-10-30 09:50:32.563390927 -0400 ++++ EMBOSS-6.6.0/emboss/epscan.c 2015-10-30 09:50:32.563390927 -0400 +@@ -0,0 +1,481 @@ ++/* @source pscan application ++** ++** Reports fingerprints in a protein sequence ++** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk) ++** @@ ++** ++** This program is free software; you can redistribute it and/or ++** modify it under the terms of the GNU General Public License ++** as published by the Free Software Foundation; either version 2 ++** of the License, or (at your option) any later version. ++** ++** This program is distributed in the hope that it will be useful, ++** but WITHOUT ANY WARRANTY; without even the implied warranty of ++** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++** GNU General Public License for more details. ++** ++** You should have received a copy of the GNU General Public License ++** along with this program; if not, write to the Free Software ++** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. ++******************************************************************************/ ++ ++#include "emboss.h" ++ ++ ++ ++ ++static void pscan_print_hits(AjPFile outf, AjPList l, ajuint nmotifs, ++ ajuint begin); ++ ++ ++ ++ ++/* @prog pscan **************************************************************** ++** ++** Scans proteins using PRINTS ++** ++******************************************************************************/ ++ ++int main(int argc, char **argv) ++{ ++ AjPSeqall seqall; ++ AjPSeq seq = NULL; ++ AjPFile outf = NULL; ++ ajint begin; ++ ajint end; ++ ajuint emin; ++ ajuint emax; ++ ++ AjPFile mfile = NULL; ++ EmbPMatPrints s = NULL; ++ AjPList l = NULL; ++ AjPStr strand = NULL; ++ AjPStr substr = NULL; ++ AjPStr name = NULL; ++ ++ AjBool all; ++ AjBool ordered; ++ ++ ajint hits; ++ ajint nmotifs; ++ ++ embInit("pscan", argc, argv); ++ ++ seqall = ajAcdGetSeqall("sequence"); ++ outf = ajAcdGetOutfile("outfile"); ++ emin = ajAcdGetInt("emin"); ++ emax = ajAcdGetInt("emax"); ++ ++ substr = ajStrNew(); ++ name = ajStrNew(); ++ ++ all = ordered = ajTrue; ++ ++ ++ ++ while(ajSeqallNext(seqall, &seq)) ++ { ++ begin = ajSeqallGetseqBegin(seqall); ++ end = ajSeqallGetseqEnd(seqall); ++ ++ ajStrAssignC(&name,ajSeqGetNameC(seq)); ++ strand = ajSeqGetSeqCopyS(seq); ++ ++ ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); ++ ++ nmotifs = 0; ++ ajDebug("pscan sequence '%S'\n", ajSeqGetNameS(seq)); ++ embMatPrintsInit(&mfile); ++ ajDebug("pscan prints file '%F'\n", mfile); ++ l = ajListNew(); ++ while((s = embMatProtReadInt(mfile))) ++ { ++ ajDebug("pscan file '%F' read\n", mfile); ++ if(s->n >= emin && s->n <= emax) ++ { ++ hits=embMatProtScanInt(substr,name,s,&l,&all,&ordered, ++ 1); ++ if(hits) ++ ++nmotifs; ++ } ++ embMatProtDelInt(&s); ++ } ++ ++ pscan_print_hits(outf, l, nmotifs, begin); ++ ajListFree(&l); ++ ++ ++ ajStrDel(&strand); ++ ajFileClose(&mfile); ++ } ++ ++ ajStrDel(&substr); ++ ajStrDel(&name); ++ ++ ajSeqallDel(&seqall); ++ ajSeqDel(&seq); ++ ajFileClose(&outf); ++ ++ embExit(); ++ ++ return 0; ++} ++ ++ ++ ++ ++/* @funcstatic pscan_print_hits *********************************************** ++** ++** Undocumented. ++** ++** @param [u] outf [AjPFile] outfile ++** @param [u] l [AjPList] hits ++** @param [r] nmotifs [ajuint] number of hits ++** @param [r] begin [ajuint] start position ++** @@ ++******************************************************************************/ ++ ++static void pscan_print_hits(AjPFile outf, AjPList l, ajuint nmotifs, ++ ajuint begin) ++{ ++ EmbPMatMatch mm; ++ ajuint i; ++ ajuint j; ++ AjBool found; ++ ajuint nleft; ++ ajuint maxelem = 0; ++ ajuint maxhpm; ++ ajuint hpm = 0; ++ ++ nleft = nmotifs; ++ ++ ++ ajFmtPrintF(outf,"\n\nCLASS 1\n"); ++ ajFmtPrintF(outf,"Fingerprints with all elements in order\n\n"); ++ ++ ++ found = ajTrue; ++ ++ while(found && nleft) ++ { ++ found = ajFalse; ++ maxelem = 0; ++ for(i=0;iall && mm->ordered) ++ { ++ maxelem = AJMAX(maxelem,mm->n); ++ found = ajTrue; ++ } ++ hpm = mm->hpm; ++ ++ ajListPushAppend(l,(void *)mm); ++ for(j=1;jhpm; ++ ++ if(mm->all && mm->ordered && maxelem==mm->n) ++ break; ++ ajListPushAppend(l,(void *)mm); ++ ++ for(j=1;jall && mm->ordered && maxelem==mm->n) ++ { ++ ajFmtPrintF(outf,"Fingerprint %s Elements %d\n", ++ ajStrGetPtr(mm->cod),mm->n); ++ ajFmtPrintF(outf," Accession number %s\n", ++ ajStrGetPtr(mm->acc)); ++ ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit)); ++ ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n", ++ mm->element+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ embMatMatchDel(&mm); ++ } ++ ++ for(i=1;ielement+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ embMatMatchDel(&mm); ++ } ++ ++ --nleft; ++ } ++ ++ } ++ ++ ajFmtPrintF(outf,"\n\nCLASS 2\n"); ++ ajFmtPrintF(outf,"All elements match but not all in the " ++ "correct order\n\n"); ++ ++ found = ajTrue; ++ ++ while(found && nleft) ++ { ++ found = ajFalse; ++ maxelem = 0; ++ ++ for(i=0;iall) ++ { ++ maxelem = AJMAX(maxelem,mm->n); ++ found = ajTrue; ++ } ++ hpm = mm->hpm; ++ ajListPushAppend(l,(void *)mm); ++ ++ for(j=1;jhpm; ++ if(mm->all && maxelem==mm->n) ++ break; ++ ajListPushAppend(l,(void *)mm); ++ ++ for(j=1;jall && maxelem==mm->n) ++ { ++ ajFmtPrintF(outf,"Fingerprint %s Elements %d\n", ++ ajStrGetPtr(mm->cod),mm->n); ++ ajFmtPrintF(outf," Accession number %s\n", ++ ajStrGetPtr(mm->acc)); ++ ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit)); ++ ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n", ++ mm->element+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ embMatMatchDel(&mm); ++ } ++ ++ for(i=1;ielement+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ embMatMatchDel(&mm); ++ } ++ ++ --nleft; ++ } ++ ++ } ++ ++ ++ ++ ++ ajFmtPrintF(outf,"\n\nCLASS 3\n"); ++ ajFmtPrintF(outf, ++ "Not all elements match but those that do are in order\n\n"); ++ ++ found = ajTrue; ++ ++ while(found && nleft) ++ { ++ found = ajFalse; ++ maxhpm = 0; ++ for(i=0;iordered) ++ { ++ maxhpm = AJMAX(maxelem,mm->hpm); ++ found = ajTrue; ++ } ++ hpm = mm->hpm; ++ ajListPushAppend(l,(void *)mm); ++ ++ for(j=1;jhpm; ++ ++ if(mm->ordered && maxhpm==mm->hpm) ++ break; ++ ajListPushAppend(l,(void *)mm); ++ ++ for(j=1;jordered && maxhpm==mm->hpm) ++ { ++ ajFmtPrintF(outf,"Fingerprint %s Elements %d\n", ++ ajStrGetPtr(mm->cod),mm->n); ++ ajFmtPrintF(outf," Accession number %s\n", ++ ajStrGetPtr(mm->acc)); ++ ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit)); ++ ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n", ++ mm->element+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ ++ embMatMatchDel(&mm); ++ } ++ ++ for(i=1;ielement+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ embMatMatchDel(&mm); ++ } ++ ++ --nleft; ++ } ++ ++ } ++ ++ ++ ++ ++ ajFmtPrintF(outf,"\n\nCLASS 4\n"); ++ ajFmtPrintF(outf, ++ "Remaining partial matches\n\n"); ++ ++ found = ajTrue; ++ ++ while(found && nleft) ++ { ++ found = ajFalse; ++ maxhpm = 0; ++ ++ for(i=0;ihpm); ++ found = ajTrue; ++ ++ hpm = mm->hpm; ++ ajListPushAppend(l,(void *)mm); ++ for(j=1;jhpm; ++ ++ if(maxhpm==mm->hpm) ++ break; ++ ajListPushAppend(l,(void *)mm); ++ ++ for(j=1;jhpm) ++ { ++ ajFmtPrintF(outf,"Fingerprint %s Elements %d\n", ++ ajStrGetPtr(mm->cod),mm->n); ++ ajFmtPrintF(outf," Accession number %s\n", ++ ajStrGetPtr(mm->acc)); ++ ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit)); ++ ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n", ++ mm->element+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ ++ embMatMatchDel(&mm); ++ } ++ ++ for(i=1;ielement+1, mm->thresh, mm->score); ++ ajFmtPrintF(outf," Start position %d Length %d\n", ++ mm->start+begin,mm->len); ++ ++ embMatMatchDel(&mm); ++ } ++ ++ --nleft; ++ } ++ ++ } ++ ++ ++ while(ajListPop(l,(void **)&mm)) ++ if(mm) ++ embMatMatchDel(&mm); ++ ++ return; ++} +diff -up EMBOSS-6.6.0/emboss/Makefile.am.fixconflict EMBOSS-6.6.0/emboss/Makefile.am +--- EMBOSS-6.6.0/emboss/Makefile.am.fixconflict 2015-10-30 09:50:32.554390990 -0400 ++++ EMBOSS-6.6.0/emboss/Makefile.am 2015-10-30 09:51:26.065016794 -0400 +@@ -309,7 +309,7 @@ profit \ + prophecy \ + prophet \ + prosextract \ +-pscan \ ++epscan \ + psiphi \ + rebaseextract \ + recoder \ +@@ -587,7 +587,7 @@ profit_SOURCES = profit.c + prophecy_SOURCES = prophecy.c + prophet_SOURCES = prophet.c + prosextract_SOURCES = prosextract.c +-pscan_SOURCES = pscan.c ++epscan_SOURCES = epscan.c + psiphi_SOURCES = psiphi.c + rebaseextract_SOURCES = rebaseextract.c + recoder_SOURCES = recoder.c +diff -up EMBOSS-6.6.0/emboss/Makefile.in.fixconflict EMBOSS-6.6.0/emboss/Makefile.in +--- EMBOSS-6.6.0/emboss/Makefile.in.fixconflict 2013-07-15 17:27:30.000000000 -0400 ++++ EMBOSS-6.6.0/emboss/Makefile.in 2015-10-30 09:50:32.565390913 -0400 +@@ -142,7 +142,7 @@ bin_PROGRAMS = aaindexextract$(EXEEXT) a + plotorf$(EXEEXT) polydot$(EXEEXT) preg$(EXEEXT) \ + prettyplot$(EXEEXT) prettyseq$(EXEEXT) primersearch$(EXEEXT) \ + printsextract$(EXEEXT) profit$(EXEEXT) prophecy$(EXEEXT) \ +- prophet$(EXEEXT) prosextract$(EXEEXT) pscan$(EXEEXT) \ ++ prophet$(EXEEXT) prosextract$(EXEEXT) epscan$(EXEEXT) \ + psiphi$(EXEEXT) rebaseextract$(EXEEXT) recoder$(EXEEXT) \ + redata$(EXEEXT) refseqget$(EXEEXT) remap$(EXEEXT) \ + restover$(EXEEXT) restrict$(EXEEXT) revseq$(EXEEXT) \ +@@ -1993,10 +1993,10 @@ prosextract_DEPENDENCIES = ../nucleus/li + ../ajax/core/libajax.la $(am__append_3) \ + ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ + $(am__DEPENDENCIES_1) +-am_pscan_OBJECTS = pscan.$(OBJEXT) +-pscan_OBJECTS = $(am_pscan_OBJECTS) +-pscan_LDADD = $(LDADD) +-pscan_DEPENDENCIES = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ ++am_epscan_OBJECTS = epscan.$(OBJEXT) ++epscan_OBJECTS = $(am_epscan_OBJECTS) ++epscan_LDADD = $(LDADD) ++epscan_DEPENDENCIES = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ + ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ + ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ + $(am__append_3) ../ajax/pcre/libepcre.la \ +@@ -2821,7 +2821,7 @@ SOURCES = $(aaindexextract_SOURCES) $(ab + $(preg_SOURCES) $(prettyplot_SOURCES) $(prettyseq_SOURCES) \ + $(prima_SOURCES) $(primers_SOURCES) $(primersearch_SOURCES) \ + $(printsextract_SOURCES) $(profit_SOURCES) $(prophecy_SOURCES) \ +- $(prophet_SOURCES) $(prosextract_SOURCES) $(pscan_SOURCES) \ ++ $(prophet_SOURCES) $(prosextract_SOURCES) $(epscan_SOURCES) \ + $(psiphi_SOURCES) $(rebaseextract_SOURCES) $(recoder_SOURCES) \ + $(redata_SOURCES) $(refseqget_SOURCES) $(remap_SOURCES) \ + $(restover_SOURCES) $(restrict_SOURCES) $(revseq_SOURCES) \ +@@ -2934,7 +2934,7 @@ DIST_SOURCES = $(aaindexextract_SOURCES) + $(preg_SOURCES) $(prettyplot_SOURCES) $(prettyseq_SOURCES) \ + $(prima_SOURCES) $(primers_SOURCES) $(primersearch_SOURCES) \ + $(printsextract_SOURCES) $(profit_SOURCES) $(prophecy_SOURCES) \ +- $(prophet_SOURCES) $(prosextract_SOURCES) $(pscan_SOURCES) \ ++ $(prophet_SOURCES) $(prosextract_SOURCES) $(epscan_SOURCES) \ + $(psiphi_SOURCES) $(rebaseextract_SOURCES) $(recoder_SOURCES) \ + $(redata_SOURCES) $(refseqget_SOURCES) $(remap_SOURCES) \ + $(restover_SOURCES) $(restrict_SOURCES) $(revseq_SOURCES) \ +@@ -3414,7 +3414,7 @@ profit_SOURCES = profit.c + prophecy_SOURCES = prophecy.c + prophet_SOURCES = prophet.c + prosextract_SOURCES = prosextract.c +-pscan_SOURCES = pscan.c ++epscan_SOURCES = epscan.c + psiphi_SOURCES = psiphi.c + rebaseextract_SOURCES = rebaseextract.c + recoder_SOURCES = recoder.c +@@ -4266,9 +4266,9 @@ prophet$(EXEEXT): $(prophet_OBJECTS) $(p + prosextract$(EXEEXT): $(prosextract_OBJECTS) $(prosextract_DEPENDENCIES) $(EXTRA_prosextract_DEPENDENCIES) + @rm -f prosextract$(EXEEXT) + $(LINK) $(prosextract_OBJECTS) $(prosextract_LDADD) $(LIBS) +-pscan$(EXEEXT): $(pscan_OBJECTS) $(pscan_DEPENDENCIES) $(EXTRA_pscan_DEPENDENCIES) +- @rm -f pscan$(EXEEXT) +- $(LINK) $(pscan_OBJECTS) $(pscan_LDADD) $(LIBS) ++epscan$(EXEEXT): $(epscan_OBJECTS) $(epscan_DEPENDENCIES) $(EXTRA_epscan_DEPENDENCIES) ++ @rm -f epscan$(EXEEXT) ++ $(LINK) $(epscan_OBJECTS) $(epscan_LDADD) $(LIBS) + psiphi$(EXEEXT): $(psiphi_OBJECTS) $(psiphi_DEPENDENCIES) $(EXTRA_psiphi_DEPENDENCIES) + @rm -f psiphi$(EXEEXT) + $(LINK) $(psiphi_OBJECTS) $(psiphi_LDADD) $(LIBS) +@@ -4748,7 +4748,7 @@ distclean-compile: + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/prophecy.Po@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/prophet.Po@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/prosextract.Po@am__quote@ +-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pscan.Po@am__quote@ ++@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/epscan.Po@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/psiphi.Po@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rebaseextract.Po@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/recoder.Po@am__quote@ diff --git a/EMBOSS-6.6.0-no-update.patch b/EMBOSS-6.6.0-no-update.patch new file mode 100644 index 0000000..3107f9a --- /dev/null +++ b/EMBOSS-6.6.0-no-update.patch @@ -0,0 +1,9 @@ +diff -up EMBOSS-6.6.0/Makefile.am.noupdate EMBOSS-6.6.0/Makefile.am +--- EMBOSS-6.6.0/Makefile.am.noupdate 2015-10-30 09:59:36.183032495 -0400 ++++ EMBOSS-6.6.0/Makefile.am 2015-10-30 09:59:45.889975922 -0400 +@@ -34,4 +34,4 @@ dist-hook: + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + + install-exec-hook: +- $(bindir)/embossupdate ++### $(bindir)/embossupdate diff --git a/EMBOSS-6.6.0-system-expat.patch b/EMBOSS-6.6.0-system-expat.patch new file mode 100644 index 0000000..1392289 --- /dev/null +++ b/EMBOSS-6.6.0-system-expat.patch @@ -0,0 +1,19 @@ +diff -up EMBOSS-6.6.0/configure.in.system-expat EMBOSS-6.6.0/configure.in +--- EMBOSS-6.6.0/configure.in.system-expat 2015-10-30 09:30:20.978720930 -0400 ++++ EMBOSS-6.6.0/configure.in 2015-10-30 09:31:33.117227536 -0400 +@@ -810,6 +810,7 @@ AC_ARG_ENABLE([systemlibs], + [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) + if test "x${enable_systemlibs}" = "xyes" ; then + AC_CHECK_LIB(pcre, pcre_compile) ++ AC_CHECK_LIB(expat, XML_ParserCreate) + fi + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + +@@ -962,7 +963,6 @@ AC_CONFIG_FILES([Makefile + ajax/ajaxdb/Makefile + ajax/core/Makefile + ajax/ensembl/Makefile +- ajax/expat/Makefile + ajax/graphics/Makefile + ajax/zlib/Makefile + doc/Makefile diff --git a/EMBOSS-6.6.0-system-pcre.patch b/EMBOSS-6.6.0-system-pcre.patch new file mode 100644 index 0000000..018642b --- /dev/null +++ b/EMBOSS-6.6.0-system-pcre.patch @@ -0,0 +1,228 @@ +diff -up EMBOSS-6.6.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/acd/Makefile.am +--- EMBOSS-6.6.0/ajax/acd/Makefile.am.system-pcre 2013-07-15 17:25:27.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/acd/Makefile.am 2015-10-30 09:48:28.603257770 -0400 +@@ -7,10 +7,10 @@ libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVW + libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics +-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot + libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) +diff -up EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am +--- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am.system-pcre 2013-07-15 17:25:28.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am 2015-10-30 09:48:28.603257770 -0400 +@@ -5,10 +5,10 @@ lib_LTLIBRARIES = libajaxdb.la + libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) + + libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl +-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot + libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) +diff -up EMBOSS-6.6.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.6.0/ajax/core/ajreg.h +--- EMBOSS-6.6.0/ajax/core/ajreg.h.system-pcre 2011-10-18 10:23:40.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/core/ajreg.h 2015-10-30 09:48:28.603257770 -0400 +@@ -39,9 +39,8 @@ + #include "ajdefine.h" + #include "ajstr.h" + +-#include "pcre_config.h" +-#include "pcre_internal.h" +-#include "pcreposix.h" ++#include ++#include + + AJ_BEGIN_DECLS + +@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS + + typedef struct AjSRegexp + { +- real_pcre *pcre; ++ struct real_pcre *pcre; + pcre_extra *extra; + int *ovector; + const char* orig; +diff -up EMBOSS-6.6.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/core/Makefile.am +--- EMBOSS-6.6.0/ajax/core/Makefile.am.system-pcre 2013-07-15 17:25:28.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/core/Makefile.am 2015-10-30 09:49:05.159002139 -0400 +@@ -4,10 +4,11 @@ lib_LTLIBRARIES = libajax.la + + libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) + +-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajax_la_CPPFLAGS = + if !ESYSTEMLIBS + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot + libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) +diff -up EMBOSS-6.6.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/ensembl/Makefile.am +--- EMBOSS-6.6.0/ajax/ensembl/Makefile.am.system-pcre 2013-07-15 17:25:31.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am 2015-10-30 09:49:24.304868253 -0400 +@@ -4,10 +4,11 @@ lib_LTLIBRARIES = libensembl.la + + libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) + +-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libensembl_la_CPPFLAGS = + if !ESYSTEMLIBS + libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot + libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) +diff -up EMBOSS-6.6.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/graphics/Makefile.am +--- EMBOSS-6.6.0/ajax/graphics/Makefile.am.system-pcre 2013-07-15 17:25:33.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/graphics/Makefile.am 2015-10-30 09:49:52.210673110 -0400 +@@ -4,9 +4,10 @@ lib_LTLIBRARIES = libajaxg.la + + libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) + +-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajaxg_la_CPPFLAGS = + if !ESYSTEMLIBS + libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat ++libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot + libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) +diff -up EMBOSS-6.6.0/ajax/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/Makefile.am +--- EMBOSS-6.6.0/ajax/Makefile.am.system-pcre 2011-08-25 15:45:55.000000000 -0400 ++++ EMBOSS-6.6.0/ajax/Makefile.am 2015-10-30 09:48:28.604257763 -0400 +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + +-SUBDIRS = pcre ++SUBDIRS = + if !ESYSTEMLIBS +-SUBDIRS += expat zlib ++SUBDIRS += expat zlib pcre + endif + SUBDIRS += core graphics ensembl ajaxdb acd +diff -up EMBOSS-6.6.0/configure.in.system-pcre EMBOSS-6.6.0/configure.in +--- EMBOSS-6.6.0/configure.in.system-pcre 2013-07-15 17:25:27.000000000 -0400 ++++ EMBOSS-6.6.0/configure.in 2015-10-30 09:48:28.604257763 -0400 +@@ -630,31 +630,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- + dnl Define where the EMBOSS package is located + AC_SUBST([AJAX_FIXED_ROOT]) + AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" +@@ -743,19 +718,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- + + + # Enable debugging: --enable-debug, sets CFLAGS +@@ -846,7 +808,9 @@ AS_IF([test "x${enable_large}" = "xno"], + + AC_ARG_ENABLE([systemlibs], + [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) +- ++if test "x${enable_systemlibs}" = "xyes" ; then ++ AC_CHECK_LIB(pcre, pcre_compile) ++fi + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + +@@ -1000,7 +964,6 @@ AC_CONFIG_FILES([Makefile + ajax/ensembl/Makefile + ajax/expat/Makefile + ajax/graphics/Makefile +- ajax/pcre/Makefile + ajax/zlib/Makefile + doc/Makefile + doc/manuals/Makefile +diff -up EMBOSS-6.6.0/emboss/Makefile.am.system-pcre EMBOSS-6.6.0/emboss/Makefile.am +--- EMBOSS-6.6.0/emboss/Makefile.am.system-pcre 2013-07-15 17:25:46.000000000 -0400 ++++ EMBOSS-6.6.0/emboss/Makefile.am 2015-10-30 09:48:28.605257756 -0400 +@@ -30,10 +30,10 @@ AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd + AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb + AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl + AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics +-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS + AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat + AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + AM_CPPFLAGS += -I$(top_srcdir)/nucleus + AM_CPPFLAGS += -I$(top_srcdir)/plplot +@@ -49,8 +49,8 @@ LDADD += ../ajax/core/libajax.la + if !ESYSTEMLIBS + LDADD += ../ajax/zlib/libezlib.la + LDADD += ../ajax/expat/libeexpat.la +-endif + LDADD += ../ajax/pcre/libepcre.la ++endif + LDADD += ../plplot/libeplplot.la + LDADD += $(XLIB) + +diff -up EMBOSS-6.6.0/nucleus/Makefile.am.system-pcre EMBOSS-6.6.0/nucleus/Makefile.am +--- EMBOSS-6.6.0/nucleus/Makefile.am.system-pcre 2013-07-15 17:25:50.000000000 -0400 ++++ EMBOSS-6.6.0/nucleus/Makefile.am 2015-10-30 09:48:28.605257756 -0400 +@@ -11,10 +11,10 @@ endif + endif + + libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot +-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + endif + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl diff --git a/EMBOSS-6.6.0-system-zlib.patch b/EMBOSS-6.6.0-system-zlib.patch new file mode 100644 index 0000000..84858e0 --- /dev/null +++ b/EMBOSS-6.6.0-system-zlib.patch @@ -0,0 +1,19 @@ +diff -up EMBOSS-6.6.0/configure.in.system-zlib EMBOSS-6.6.0/configure.in +--- EMBOSS-6.6.0/configure.in.system-zlib 2015-10-30 09:32:02.595043840 -0400 ++++ EMBOSS-6.6.0/configure.in 2015-10-30 09:32:48.225796757 -0400 +@@ -811,6 +811,7 @@ AC_ARG_ENABLE([systemlibs], + if test "x${enable_systemlibs}" = "xyes" ; then + AC_CHECK_LIB(pcre, pcre_compile) + AC_CHECK_LIB(expat, XML_ParserCreate) ++ AC_CHECK_LIB(z, compress) + fi + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + +@@ -964,7 +965,6 @@ AC_CONFIG_FILES([Makefile + ajax/core/Makefile + ajax/ensembl/Makefile + ajax/graphics/Makefile +- ajax/zlib/Makefile + doc/Makefile + doc/manuals/Makefile + doc/programs/Makefile