diff --git a/EMBOSS-6.4.0-fix-conflict-with-pscan.patch b/EMBOSS-6.4.0-fix-conflict-with-pscan.patch new file mode 100644 index 0000000..cc54e98 --- /dev/null +++ b/EMBOSS-6.4.0-fix-conflict-with-pscan.patch @@ -0,0 +1,707 @@ +diff -up EMBOSS-6.4.0/emboss/acd/epscan.acd.fixconflict EMBOSS-6.4.0/emboss/acd/epscan.acd +--- EMBOSS-6.4.0/emboss/acd/epscan.acd.fixconflict 2012-02-27 09:53:58.673872826 -0500 ++++ EMBOSS-6.4.0/emboss/acd/epscan.acd 2012-02-27 09:54:48.345441143 -0500 +@@ -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-6.4.0/emboss/acd/Makefile.am.fixconflict EMBOSS-6.4.0/emboss/acd/Makefile.am +--- EMBOSS-6.4.0/emboss/acd/Makefile.am.fixconflict 2012-02-27 09:46:48.379612489 -0500 ++++ EMBOSS-6.4.0/emboss/acd/Makefile.am 2012-02-27 09:46:59.796513263 -0500 +@@ -54,7 +54,7 @@ pkgdata2_DATA = needle.acd needleall.acd + pepwheel.acd pepwindow.acd pepwindowall.acd plotcon.acd plotorf.acd \ + polydot.acd preg.acd prettyplot.acd prettyseq.acd \ + primersearch.acd printsextract.acd profit.acd \ +- prophecy.acd prophet.acd prosextract.acd pscan.acd psiphi.acd \ ++ prophecy.acd prophet.acd prosextract.acd epscan.acd psiphi.acd \ + rebaseextract.acd recoder.acd redata.acd remap.acd restover.acd \ + restrict.acd revseq.acd seealso.acd \ + seqcount.acd seqmatchall.acd \ +diff -up EMBOSS-6.4.0/emboss/acd/Makefile.fixconflict EMBOSS-6.4.0/emboss/acd/Makefile +--- EMBOSS-6.4.0/emboss/acd/Makefile.fixconflict 2012-02-27 09:47:30.481246583 -0500 ++++ EMBOSS-6.4.0/emboss/acd/Makefile 2012-02-27 09:47:33.853217278 -0500 +@@ -299,7 +299,7 @@ pkgdata2_DATA = needle.acd needleall.acd + pepwheel.acd pepwindow.acd pepwindowall.acd plotcon.acd plotorf.acd \ + polydot.acd preg.acd prettyplot.acd prettyseq.acd \ + primersearch.acd printsextract.acd profit.acd \ +- prophecy.acd prophet.acd prosextract.acd pscan.acd psiphi.acd \ ++ prophecy.acd prophet.acd prosextract.acd epscan.acd psiphi.acd \ + rebaseextract.acd recoder.acd redata.acd remap.acd restover.acd \ + restrict.acd revseq.acd seealso.acd \ + seqcount.acd seqmatchall.acd \ +diff -up EMBOSS-6.4.0/emboss/acd/Makefile.in.fixconflict EMBOSS-6.4.0/emboss/acd/Makefile.in +--- EMBOSS-6.4.0/emboss/acd/Makefile.in.fixconflict 2012-02-27 09:47:10.357421484 -0500 ++++ EMBOSS-6.4.0/emboss/acd/Makefile.in 2012-02-27 09:47:16.506368036 -0500 +@@ -299,7 +299,7 @@ pkgdata2_DATA = needle.acd needleall.acd + pepwheel.acd pepwindow.acd pepwindowall.acd plotcon.acd plotorf.acd \ + polydot.acd preg.acd prettyplot.acd prettyseq.acd \ + primersearch.acd printsextract.acd profit.acd \ +- prophecy.acd prophet.acd prosextract.acd pscan.acd psiphi.acd \ ++ prophecy.acd prophet.acd prosextract.acd epscan.acd psiphi.acd \ + rebaseextract.acd recoder.acd redata.acd remap.acd restover.acd \ + restrict.acd revseq.acd seealso.acd \ + seqcount.acd seqmatchall.acd \ +diff -up EMBOSS-6.4.0/emboss/acd/printsextract.acd.fixconflict EMBOSS-6.4.0/emboss/acd/printsextract.acd +--- EMBOSS-6.4.0/emboss/acd/printsextract.acd.fixconflict 2012-02-27 09:48:16.922842970 -0500 ++++ EMBOSS-6.4.0/emboss/acd/printsextract.acd 2012-02-27 09:48:27.680749468 -0500 +@@ -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-6.4.0/emboss/data/edamtoacd.dat.fixconflict EMBOSS-6.4.0/emboss/data/edamtoacd.dat +--- EMBOSS-6.4.0/emboss/data/edamtoacd.dat.fixconflict 2012-02-27 09:47:52.084058836 -0500 ++++ EMBOSS-6.4.0/emboss/data/edamtoacd.dat 2012-02-27 09:47:57.107015183 -0500 +@@ -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-6.4.0/emboss/epscan.c.fixconflict EMBOSS-6.4.0/emboss/epscan.c +--- EMBOSS-6.4.0/emboss/epscan.c.fixconflict 2012-02-27 09:48:44.891599888 -0500 ++++ EMBOSS-6.4.0/emboss/epscan.c 2012-02-27 09:48:40.234640361 -0500 +@@ -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-6.4.0/emboss/Makefile.am.fixconflict EMBOSS-6.4.0/emboss/Makefile.am +--- EMBOSS-6.4.0/emboss/Makefile.am.fixconflict 2012-02-27 09:48:55.526507467 -0500 ++++ EMBOSS-6.4.0/emboss/Makefile.am 2012-02-27 09:52:54.611429591 -0500 +@@ -80,7 +80,7 @@ pepwheel pepwindow pepwindowall \ + plotcon plotorf polydot preg \ + prettyplot prettyseq primersearch printsextract \ + profit prophecy prophet \ +-prosextract pscan psiphi \ ++prosextract epscan psiphi \ + rebaseextract recoder redata remap \ + restover restrict revseq \ + seealso seqcount seqmatchall seqret seqretsetall seqretsplit \ +@@ -301,7 +301,7 @@ profit_SOURCES = profit.c + prophecy_SOURCES = prophecy.c + prophet_SOURCES = prophet.c + prosextract_SOURCES = prosextract.c +-pscan_SOURCES = pscan.c ++epscan_SOURCES = pscan.c + psiphi_SOURCES = psiphi.c + rebaseextract_SOURCES = rebaseextract.c + recoder_SOURCES = recoder.c +diff -up EMBOSS-6.4.0/emboss/Makefile.in.fixconflict EMBOSS-6.4.0/emboss/Makefile.in +--- EMBOSS-6.4.0/emboss/Makefile.in.fixconflict 2012-02-27 09:49:12.123363211 -0500 ++++ EMBOSS-6.4.0/emboss/Makefile.in 2012-02-27 09:52:34.681602796 -0500 +@@ -109,7 +109,7 @@ 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$(EXEEXT) remap$(EXEEXT) restover$(EXEEXT) \ + restrict$(EXEEXT) revseq$(EXEEXT) seealso$(EXEEXT) \ +@@ -1837,10 +1837,10 @@ prosextract_DEPENDENCIES = ../nucleus/li + ../ajax/ensembl/libensembl.la ../ajax/graphics/libajaxg.la \ + ../ajax/core/libajax.la $(EXTRA_LDS) ../ajax/pcre/libepcre.la \ + ../plplot/libeplplot.la $(am__DEPENDENCIES_1) +-am_pscan_OBJECTS = pscan.$(OBJEXT) +-pscan_OBJECTS = $(am_pscan_OBJECTS) +-pscan_LDADD = $(LDADD) +-pscan_DEPENDENCIES = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ ++am_epscan_OBJECTS = pscan.$(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 \ + $(EXTRA_LDS) ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ +@@ -2592,7 +2592,7 @@ 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) $(remap_SOURCES) $(restover_SOURCES) \ + $(restrict_SOURCES) $(revseq_SOURCES) $(seealso_SOURCES) \ +@@ -2701,7 +2701,7 @@ 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) $(remap_SOURCES) $(restover_SOURCES) \ + $(restrict_SOURCES) $(revseq_SOURCES) $(seealso_SOURCES) \ +@@ -3172,7 +3172,7 @@ profit_SOURCES = profit.c + prophecy_SOURCES = prophecy.c + prophet_SOURCES = prophet.c + prosextract_SOURCES = prosextract.c +-pscan_SOURCES = pscan.c ++epscan_SOURCES = pscan.c + psiphi_SOURCES = psiphi.c + rebaseextract_SOURCES = rebaseextract.c + recoder_SOURCES = recoder.c +@@ -3990,9 +3990,9 @@ prophet$(EXEEXT): $(prophet_OBJECTS) $(p + prosextract$(EXEEXT): $(prosextract_OBJECTS) $(prosextract_DEPENDENCIES) + @rm -f prosextract$(EXEEXT) + $(LINK) $(prosextract_OBJECTS) $(prosextract_LDADD) $(LIBS) +-pscan$(EXEEXT): $(pscan_OBJECTS) $(pscan_DEPENDENCIES) +- @rm -f pscan$(EXEEXT) +- $(LINK) $(pscan_OBJECTS) $(pscan_LDADD) $(LIBS) ++epscan$(EXEEXT): $(epscan_OBJECTS) $(epscan_DEPENDENCIES) ++ @rm -f epscan$(EXEEXT) ++ $(LINK) $(epscan_OBJECTS) $(epscan_LDADD) $(LIBS) + psiphi$(EXEEXT): $(psiphi_OBJECTS) $(psiphi_DEPENDENCIES) + @rm -f psiphi$(EXEEXT) + $(LINK) $(psiphi_OBJECTS) $(psiphi_LDADD) $(LIBS) +@@ -4456,7 +4456,7 @@ distclean-compile: + @AMDEP_TRUE@@am__include@ @am__quote@./$(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.spec b/EMBOSS.spec index f58d887..a25ec77 100644 --- a/EMBOSS.spec +++ b/EMBOSS.spec @@ -3,6 +3,8 @@ # This would involve packaging jalview (specifically, the Applet) # The jalview code has a LOT of bundled pre-built jars. +# NOTE: If EMBOSS updates, please ensure that Patch9 is properly redone to match. +# Notably, emboss/acd/epscan.acd should stay in sync with pscan.acd. #jemboss is disabled by default due to the fact it bundles a few .jar files which are not built from source. %bcond_with jemboss @@ -18,7 +20,7 @@ Name: EMBOSS Version: 6.4.0 -Release: 4%{?dist} +Release: 5%{?dist} Summary: The European Molecular Biology Open Software Suite # Files under jemboss/, ajax/ensembl/ are LGPLv2+ @@ -51,6 +53,10 @@ Patch5: EMBOSS-6.4.0-system-zlib.patch Patch7: %{name}-fedora.patch # Updated patch created on 2011-11-23. Patch8: EMBOSS-6.4.0-system-hack.patch +# Fix conflict with pscan (Fedora package, unrelated to EMBOSS) +# https://bugzilla.redhat.com/show_bug.cgi?id=797804 +# Emailed upstream on the issue on 2012-02-27 +Patch9: EMBOSS-6.4.0-fix-conflict-with-pscan.patch BuildRequires: gd-devel BuildRequires: pam-devel @@ -154,6 +160,7 @@ necessary for developing programs which will use the eplplot library. %patch7 -p0 -b .fedora %patch8 -p1 -b .system-hack +%patch9 -p1 -b .fixconflict # Remove bundled expat, pcre and zlib to make sure that system versions are used rm -rf ajax/{expat,pcre,zlib} @@ -312,6 +319,9 @@ desktop-file-install \ %{_includedir}/EMBOSS/eplplot/ %changelog +* Mon Feb 27 2012 Tom Callaway - 6.4.0-5 +- resolve conflict with pscan + * Fri Feb 10 2012 Petr Pisar - 6.4.0-4 - Rebuild against PCRE 8.30