commit: 536ecc57f40abd1f4f11c9c398df530d10838fb4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 16:37:01 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 16:37:01 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=536ecc57
sci-biology/wise: version bump, add patches from wise_2.4.1-19_debian
Dropped tcsh dependence because that is removed by a path.
We do not call 'make perl' so maybe could drop perl dependency as well?
Wether the bundled while modified hmmer-2 sources can be dropped is
not clear but it seems the only callers of hmmer-2 binaries are in
automated tests. Not sure about libhmmer.a needs.
Notably, sci-biology/hmmer-2.3.2-r4 provides /usr/lib64/libhmmer2.a
while sci-biology/hmmer-3.1_beta2 provides /usr/lib64/libhmmer.a.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/wise/files/01_welcome-csh.patch | 22 ++
sci-biology/wise/files/02_isnumber.patch | 14 +
sci-biology/wise/files/03_doc-nodycache.patch | 15 +
.../wise/files/04_wise2-pdflatex-update.patch | 38 ++
sci-biology/wise/files/06_getline.patch | 305 +++++++++++++++
sci-biology/wise/files/07_ld--as-needed.patch | 52 +++
sci-biology/wise/files/08_mayhem.patch | 103 ++++++
.../wise/files/09_dnal-add-return-statement.patch | 17 +
.../wise/files/11_consistent_manual_dates.patch | 53 +++
sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch | 301 +++++++++++++++
sci-biology/wise/files/wise-2.4.1-cflags.patch | 407 +++++++++++++++++++++
sci-biology/wise/files/wise-env | 1 +
sci-biology/wise/wise-2.4.1.ebuild | 39 +-
13 files changed, 1359 insertions(+), 8 deletions(-)
diff --git a/sci-biology/wise/files/01_welcome-csh.patch
b/sci-biology/wise/files/01_welcome-csh.patch
new file mode 100644
index 0000000..3a9057e
--- /dev/null
+++ b/sci-biology/wise/files/01_welcome-csh.patch
@@ -0,0 +1,22 @@
+Author: Philipp Benner <m...@philipp-benner.de>
+Description: Avoid dependency from csh
+
+--- wise-2.4.1.orig/src/makefile
++++ wise-2.4.1/src/makefile
+@@ -109,7 +109,7 @@
+ bin :
+ mkdir bin
+ 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
+- csh welcome.csh
++ ./welcome.csh
+
+ libs :
+ (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
+--- wise-2.4.1.orig/src/welcome.csh
++++ wise-2.4.1/src/welcome.csh
+@@ -1,4 +1,4 @@
+-#!/bin/tcsh -f
++#!/bin/sh
+
+ echo ""
+ echo "Welcome to Wise2.4"
diff --git a/sci-biology/wise/files/02_isnumber.patch
b/sci-biology/wise/files/02_isnumber.patch
new file mode 100644
index 0000000..a6ae908
--- /dev/null
+++ b/sci-biology/wise/files/02_isnumber.patch
@@ -0,0 +1,14 @@
+Author: Philipp Benner <m...@philipp-benner.de>
+Description: Replace isnumber() (which does not exist on linux) by isdigit().
+
+--- wise-2.4.1.orig/src/models/phasemodel.c
++++ wise-2.4.1/src/models/phasemodel.c
+@@ -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;
+ }
diff --git a/sci-biology/wise/files/03_doc-nodycache.patch
b/sci-biology/wise/files/03_doc-nodycache.patch
new file mode 100644
index 0000000..6fe7b18
--- /dev/null
+++ b/sci-biology/wise/files/03_doc-nodycache.patch
@@ -0,0 +1,15 @@
+Author Philipp Benner <m...@philipp-benner.de>
+Description: Documentation bugfix.
+
+--- wise-2.4.1.orig/docs/wise2.tex
++++ wise-2.4.1/docs/wise2.tex
+@@ -1617,7 +1617,8 @@
+ \item[-hithelp] more detailed help on hitlist formats
+ \item[-dymem] memory style [default/linear/explicit]
+ \item[-kbyte] memory amount to use [4000]
+-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
++\item[-dycache] implicitly cache dy matrix usage (default)
++\item[-nodycache] do not implicitly cache dy matrix usage
+ \item[-dydebug] drop into dynamite dp matrix debugger
+ \item[-paldebug] print PackAln after debugger run if used
+ \item[-help] show help options
diff --git a/sci-biology/wise/files/04_wise2-pdflatex-update.patch
b/sci-biology/wise/files/04_wise2-pdflatex-update.patch
new file mode 100644
index 0000000..bbaf286
--- /dev/null
+++ b/sci-biology/wise/files/04_wise2-pdflatex-update.patch
@@ -0,0 +1,38 @@
+Author Philipp Benner <m...@philipp-benner.de>
+Description: Make wise2.tex pdflatex compatible.
+
+--- wise-2.4.1.orig/docs/wise2.tex
++++ wise-2.4.1/docs/wise2.tex
+@@ -1,6 +1,7 @@
+
+ \documentclass{article}
+-\usepackage{epsfig}
++%\usepackage{epsfig}
++\usepackage{graphicx}
+
+ \begin{document}
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -707,8 +708,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode
+-\epsfxsize 300pt
+-\epsfbox{genewise21.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise21.eps}
++%\includegraphics[scale=0.75]{genewise21.pdf}
+ \newline
+ \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
+ arrows between them transitions. Black transitions are standard
+@@ -898,8 +900,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode
+-\epsfxsize 300pt
+-\epsfbox{genewise6.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise6.eps}
++%\includegraphics[scale=0.75]{genewise6.pdf}
+ \newline
+ \caption{GeneWise6:23}
+ \label{Figure:genewise623}
diff --git a/sci-biology/wise/files/06_getline.patch
b/sci-biology/wise/files/06_getline.patch
new file mode 100644
index 0000000..341cdae
--- /dev/null
+++ b/sci-biology/wise/files/06_getline.patch
@@ -0,0 +1,305 @@
+Author: Philipp Benner <phil...@debian.org>
+Last-Update: Sat, 31 Oct 2009 21:25:52 +0000
+Bug-Debian: http://bugs.debian.org/552821
+Description: Fixed conflicting definitions of getline().
+
+--- wise-2.4.1.orig/src/HMMer2/sqio.c
++++ wise-2.4.1/src/HMMer2/sqio.c
+@@ -213,7 +213,7 @@
+ }
+ }
+
+-/* Function: getline()
++/* Function: getline_()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++getline_(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ getline_(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ getline_(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ getline_(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ getline_(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -377,7 +377,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ getline_(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ getline_(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ getline_(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -438,7 +438,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ getline_(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ getline_(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") ==
V->sbuffer))))
+- getline(V);
++ getline_(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ getline_(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ getline_(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ getline_(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) getline_(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -587,7 +587,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ getline_(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@
+ }
+
+ do {
+- getline(V);
++ getline_(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -636,7 +636,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ getline_(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ getline_(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ getline_(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ getline_(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ getline_(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ getline_(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -816,7 +816,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ getline_(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ getline_(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ getline_(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ getline_(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/wise/files/07_ld--as-needed.patch
b/sci-biology/wise/files/07_ld--as-needed.patch
new file mode 100644
index 0000000..51ee254
--- /dev/null
+++ b/sci-biology/wise/files/07_ld--as-needed.patch
@@ -0,0 +1,52 @@
+Description: Fix FTBFS with ld --as-needed.
+Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
+
+--- wise-2.4.1.orig/src/models/makefile
++++ wise-2.4.1/src/models/makefile
+@@ -215,7 +215,7 @@
+ $(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 @@
+ $(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 @@
+
+
+ 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 @@
+ $(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)
diff --git a/sci-biology/wise/files/08_mayhem.patch
b/sci-biology/wise/files/08_mayhem.patch
new file mode 100644
index 0000000..c54c7c6
--- /dev/null
+++ b/sci-biology/wise/files/08_mayhem.patch
@@ -0,0 +1,103 @@
+Author: Philipp Benner <phil...@debian.org>
+Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
+Description: Fix run time errors detected by Mayhem
+
+--- wise-2.4.1.orig/src/models/dbac.c
++++ wise-2.4.1/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);
+--- wise-2.4.1.orig/src/models/estwise.c
++++ wise-2.4.1/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;
+
+--- wise-2.4.1.orig/src/models/genewise.c
++++ wise-2.4.1/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 ) {
+--- wise-2.4.1.orig/src/models/estwisedb.c
++++ wise-2.4.1/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;
+
+--- wise-2.4.1.orig/src/models/promoterwise.c
++++ wise-2.4.1/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]);
diff --git a/sci-biology/wise/files/09_dnal-add-return-statement.patch
b/sci-biology/wise/files/09_dnal-add-return-statement.patch
new file mode 100644
index 0000000..237e596
--- /dev/null
+++ b/sci-biology/wise/files/09_dnal-add-return-statement.patch
@@ -0,0 +1,17 @@
+Author: Dejan Latinovic <dejan.latino...@imgtec.com>
+Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
+Bug-Debian: http://bugs.debian.org/751277
+Desription: Make sure dnal has a valid return value
+ This affects a bug reported against python-biopython.
+
+--- wise-2.4.1.orig/src/models/dnal.c
++++ wise-2.4.1/src/models/dnal.c
+@@ -75,6 +75,8 @@
+
+ if( show_alb == TRUE )
+ dump_ascii_AlnBlock(alb,stdout);
++
++ return 0;
+ }
+
+
diff --git a/sci-biology/wise/files/11_consistent_manual_dates.patch
b/sci-biology/wise/files/11_consistent_manual_dates.patch
new file mode 100644
index 0000000..eaea1ee
--- /dev/null
+++ b/sci-biology/wise/files/11_consistent_manual_dates.patch
@@ -0,0 +1,53 @@
+Description: Use fixed dates for manuals.
+ These make the build reproducible. I have picked the file modificatin dates of
+ the corresponding source .tex files.
+Author: Sascha Steinbiss <sas...@steinbiss.name>
+--- a/docs/dynamite.tex
++++ b/docs/dynamite.tex
+@@ -1,4 +1,5 @@
+ \documentstyle{article}
++\pdftrailerid{}
+ \begin{document}
+
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -10,6 +11,7 @@
+ Hinxton, Cambridge CB10 1SA,\\
+ England.\\
+ Email: bir...@sanger.ac.uk}
++\date{18/6/2001}
+
+ \maketitle
+
+--- a/docs/wise2.tex
++++ b/docs/wise2.tex
+@@ -1,5 +1,6 @@
+
+ \documentclass{article}
++\pdftrailerid{}
+ %\usepackage{epsfig}
+ \usepackage{graphicx}
+
+@@ -13,6 +14,7 @@
+ Hinxton, Cambridge CB10 1SD,\\
+ England.\\
+ Email: bir...@ebi.ac.uk}
++\date{18/6/2001}
+
+ \maketitle
+
+--- a/docs/wise2api.tex
++++ b/docs/wise2api.tex
+@@ -1,4 +1,5 @@
+ \documentstyle{article}
++\pdftrailerid{}
+ \begin{document}
+
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -10,6 +11,7 @@
+ Hinxton, Cambridge CB10 1SA,\\
+ England.\\
+ Email: bir...@sanger.ac.uk}
++\date{18/6/2001}
+
+ \maketitle
+
diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
new file mode 100644
index 0000000..1ec433f
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
@@ -0,0 +1,301 @@
+diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
+--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300
++++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300
+@@ -213,7 +213,7 @@
+ }
+ }
+
+-/* Function: getline()
++/* Function: get_line()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -377,7 +377,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -438,7 +438,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") ==
V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) get_line(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -587,7 +587,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -636,7 +636,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -816,7 +816,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/wise/files/wise-2.4.1-cflags.patch
b/sci-biology/wise/files/wise-2.4.1-cflags.patch
new file mode 100644
index 0000000..705ada8
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.4.1-cflags.patch
@@ -0,0 +1,407 @@
+--- wise2.4.1/src/makefile.old 2017-01-10 15:22:43.545646202 +0000
++++ wise2.4.1/src/makefile 2017-01-10 15:23:58.484888011 +0000
+@@ -22,7 +22,7 @@
+ # Change the cc line to gcc if you get compiler errors
+ # Most likely you have a non ANSI C compiler
+ # CC = /opt/intel_cc_80/bin/icc
+-CC = cc
++CC += gcc
+
+ # These are the CFLAGS to use. These days Wise2 is inherently
+ # pthreaded, and everything is compiled with threads. However
+@@ -31,13 +31,13 @@
+
+
+ # Intel icc flags
+-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags`
++# CFLAGS = -c -O3 -axWK -ipo `pkg-config glib-2.0 --cflags`
+
+ # alpha flags (-pthread)
+-# CFLAGS = -c -O3 -pthread `glib-config --cflags`
++# CFLAGS = -c -O3 -pthread `pkg-config glib-2.0 --cflags`
+
+ # normal linux/bsd/mac flags
+-CFLAGS = -c -O3 `glib-config --cflags`
++CFLAGS += -c `pkg-config glib-2.0 --cflags`
+
+
+ EXTRALIBS = -lm
+--- wise2.4.1/src/base/makefile.old 2017-01-10 15:11:43.396368920 +0000
++++ wise2.4.1/src/base/makefile 2017-01-10 15:12:30.590885552 +0000
+@@ -20,8 +20,8 @@
+
+
+ #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH
+-CFLAGS = -c -O2 -DUNIX -pthread
+-LFLAGS = -g -lm
++CFLAGS += -c -DUNIX -pthread
++LFLAGS = -lm
+ DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
+ AR_OPTIONS = ru
+
+--- wise2.4.1/src/corba/makefile.old 2017-01-10 15:12:43.086757650 +0000
++++ wise2.4.1/src/corba/makefile 2017-01-10 15:17:24.179888689 +0000
+@@ -1,10 +1,10 @@
+
+
+-CC = cc
++CC += gcc
+ INCFLAGS = -I../base/ -I../dynlibsrc
+ #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
+-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags`
-I/usr/local/include/orbit-1.0/
+-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config
--cflags client`
++#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-I/usr/local/include/orbit-1.0/
++CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config
ORBit-2.0 --cflags`
+ LFLAGS = -L../base/ -lm -lpthread
+ AR_OPTIONS = ru
+
+@@ -14,18 +14,18 @@
+ orbit-idl hspscan_corba.idl
+
+ test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o
hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
+- cc -g -o test_server test_server.o hspscan_server_impl.o
hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o
corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a
../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o
../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP
-lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o
hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o
hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a
../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o
../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config
glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o
hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o
corba_singleton.o
+- cc -o scanwise_protein_index scanwise_protein_index.o
hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o
hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a
../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit
-lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index
scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o
hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a
`pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o
+- cc -g -o test_client test_client.o hspscan_corba-common.o
hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config
--libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o
hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a
../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP
-lORBitutil -lpthread
+
+
+ test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o
hspscan_corba_wrapper.o corba_singleton.o
+- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o
hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o
../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config
--libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o
hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o
hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a
../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP
-lORBitutil -lpthread
+
+ .c.o :
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
+--- wise2.4.1/src/dnaindex/assembly/makefile.old 2017-01-10
15:17:42.238704557 +0000
++++ wise2.4.1/src/dnaindex/assembly/makefile 2017-01-10 15:19:04.599866950
+0000
+@@ -25,11 +25,11 @@
+
+
+
+-CC = cc
+-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/
-I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
++CC += gcc
++CFLAGS += -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/
-I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags`
+
+
+-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs`
-lm
++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0
--libs` -lm
+
+
+ .c.o :
+--- wise2.4.1/src/dnaindex/makefile.old 2017-01-10 15:19:16.053750635
+0000
++++ wise2.4.1/src/dnaindex/makefile 2017-01-10 15:19:50.679398862 +0000
+@@ -27,14 +27,14 @@
+
+
+ kwise : kwise.o $(ASSEMBLY_OBJ)
+- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS)
`glib-config --libs`
++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS)
`pkg-config glib-2.0 --libs`
+
+ arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ)
+- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase
$(LFLAGS) `glib-config --libs`
++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase
$(LFLAGS) `pkg-config glib-2.0 --libs`
+
+
+ findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
+- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase
$(LFLAGS) `glib-config --libs`
++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase
$(LFLAGS) `pkg-config glib-2.0 --libs`
+
+ make_shotgun : make_shotgun.o shotgun.o
+ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase
$(LFLAGS)
+@@ -69,11 +69,11 @@
+ show_euler : show_euler.o eulerindex.o singleseqspace.o
+ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna
-lwisebase $(LFLAGS)
+
+-CC = cc
+-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/
-I../dynlibsrc/ `glib-config --cflags`
++CC += gcc
++CFLAGS += -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/
-I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
+
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0
--libs` -lm
+
+
+ .c.o :
+--- wise2.4.1/src/dynlibsrc/makefile.old 2017-01-10 15:20:08.159221406
+0000
++++ wise2.4.1/src/dynlibsrc/makefile 2017-01-10 15:21:22.739464830 +0000
+@@ -81,12 +81,12 @@
+
+
+
+-CC = cc
++CC += gcc
+ 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 += -pthread -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/
`pkg-config glib-2.0 --cflags`
++#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `pkg-config
glib-2.0 --cflags`
++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
+ #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
+ LFLAGS = -g -L../base/ -lm
+ AR_OPTIONS = ru
+@@ -148,13 +148,13 @@
+ $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o
shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
+
+ test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o
hsplookupscan.o libdyna.a
+- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o
subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
../base/libwisebase.a -lm
++ $(CC) -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o
subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
../base/libwisebase.a -lm
+
+ test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o
probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o
probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
+
+ test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o
probability.o
+- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o
compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -o test_topscore test_topscore.o codon.o sequence.o hsp.o
compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
+
+
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o
codon.o sequencedb.o complexsequence.o complexevalset.o
+--- wise2.4.1/src/external/mott/makefile.old 2017-01-10 15:21:45.914229629
+0000
++++ wise2.4.1/src/external/mott/makefile 2017-01-10 15:22:13.528950163
+0000
+@@ -14,10 +14,10 @@
+ wise2_mott_bridge.o : wise2_mott_bridge.c
+ $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
+
+-CC = cc
++CC += gcc
+
+-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c
+-LFLAGS = -g -L../base/ -lm
++CFLAGS = -DPTHREAD -c
++LFLAGS = -L../base/ -lm
+ AR_OPTIONS = ru
+
+
+--- wise2.4.1/src/models/makefile.old 2017-01-10 15:24:11.908752314 +0000
++++ wise2.4.1/src/models/makefile 2017-01-10 15:34:14.159658724 +0000
+@@ -50,6 +50,8 @@
+ proteinsw.o \
+ estquick3.o
+
++EXTRALIBS += `pkg-config glib-2.0 --libs`
++
+ all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise
sywise pseudowise promoterwise scanwise libmodel.a
+
+ libmodel.a : $(NEWG)
+@@ -180,7 +182,7 @@
+ $(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) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -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)
+@@ -192,10 +194,10 @@
+ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o
$(LFLAGS) -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 glib-2.0
--cflags` $?
+
+ hsp2aln_sw.o : hsp2aln_sw.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ scanwisep_mysql.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott
-I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c
+@@ -212,10 +214,10 @@
+
+
+ scanwisep_wiseserver.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o
-DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
++ $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o
-DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
`pkg-config glib-2.0 --libs`
+
+ 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 $(LFLAGS) -L../external/mott -L../socket
-lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
`pkg-config glib-2.0 --libs`
+
+ scanwisep_compress.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket
-I../external/mott scanwisep.c
+@@ -226,25 +228,25 @@
+
+
+ scanwisep : 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 $(LFLAGS) -L../external/mott -lmott -ldyna_glib
-ldyna -lwisebase $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib
-ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs`
-lpthread
++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib
-ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config glib-2.0
--libs` -lpthread
+
+ localcishit.o : localcishit.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ promoterwise.o : promoterwise.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o
dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o
pairwiseshortdna.o
+- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o
localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o
pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase
$(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 $(LFLAGS) -ldyna_glib -ldyna -lwisebase
$(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o
motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o
dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o
pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS)
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o
dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o
pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS)
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config glib-2.0 --libs`
-lpthread
+
+ promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o
dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o
pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o
localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o
pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
$(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs`
-lpthread
++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o
localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o
pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
$(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config glib-2.0
--libs` -lpthread
+
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
$(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread
+@@ -275,35 +277,35 @@
+ $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -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) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer
-ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config
glib-2.0 --libs`
+
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o
+- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS)
-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) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o
threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o
seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib
-ldyna -lwisebase $(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) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o
fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o
seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib
-ldyna -lwisebase $(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) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o
fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o
seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib
-ldyna -lwisebase $(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) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o
seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase
+
+
+ efgw : genewise.o $(NEWG)
+- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib
-ldyna -lwisebase $(EXTRALIBS) -lefence
++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -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) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ estwisedb : estwisedb.o $(NEWG)
+- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ edb : estwisedb.o $(NEWG)
+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer
-ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
+@@ -313,28 +315,28 @@
+
+
+ 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) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o
dnaalign.o $(LFLAGS) -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) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o
genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -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) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o
genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -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) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o
aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o
$(LFLAGS) -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) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o
genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -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) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o
genestats.o pwmdna.o geneutil.o $(LFLAGS) -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) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG)
$(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config
glib-2.0 --libs`
+
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o
mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o
localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase
$(EXTRALIBS)
+
+
+ HMMER_LIBS = ../HMMer2/
+@@ -342,14 +344,14 @@
+ HMMER_DEFINE =
+
+
+-CC = cc
++CC += gcc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/
-I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread
`glib-config --cflags`
+-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/
`glib-config --cflags`
++CFLAGS = -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config
glib-2.0 --cflags`
++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/
`pkg-config glib-2.0 --cflags`
+ #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
+
+-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config
--libs`
++LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config
glib-2.0 --libs`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+--- wise2.4.1/src/network/makefile.old 2017-01-10 15:34:31.649482055 +0000
++++ wise2.4.1/src/network/makefile 2017-01-10 15:35:11.545079297 +0000
+@@ -1,10 +1,10 @@
+
+ .SUFFIXES : .dy
+
+-CC = cc
++CC += gcc
+ 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 += -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc
-I../dnaindex `pkg-config glib-2.0 --cflags`
++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm
`pkg-config glib-2.0 --libs`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+--- wise2.4.1/src/snp/makefile.old 2017-01-10 15:35:18.714006953 +0000
++++ wise2.4.1/src/snp/makefile 2017-01-10 15:36:14.330445965 +0000
+@@ -2,12 +2,12 @@
+ .SUFFIXES : .dy
+
+
+-CC = cc
++CC += gcc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/
-I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread
`glib-config --cflags`
++CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config
glib-2.0 --cflags`
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs`
-lpthread -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0
--libs` -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) $(LDFLAGS) -o test_est test_est.o genotype.o person.o
locus_framework.o locus_model_estimators.o frequency_count.o
../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
+
+ INCFLAGS = -I../base/ -I../dynlibsrc/
+ DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
new file mode 100644
index 0000000..3f781c8
--- /dev/null
+++ b/sci-biology/wise/files/wise-env
@@ -0,0 +1 @@
+WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/wise-2.4.1.ebuild
b/sci-biology/wise/wise-2.4.1.ebuild
index 9e79232..95cd6ad 100644
--- a/sci-biology/wise/wise-2.4.1.ebuild
+++ b/sci-biology/wise/wise-2.4.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -19,21 +19,44 @@ IUSE="doc static-libs"
RDEPEND="~sci-biology/hmmer-2.3.2"
DEPEND="
${RDEPEND}
- app-shells/tcsh
dev-lang/perl
- virtual/latex-base"
+ virtual/latex-base
+ dev-libs/glib"
S="${WORKDIR}"/${PN}$(delete_version_separator 3)
-#src_prepare() {
-# epatch \
-# "${FILESDIR}"/${P}-glibc-2.10.patch \
-# "${FILESDIR}"/${P}-cflags.patch
+src_prepare() {
+ epatch "${FILESDIR}"/wise-2.2.0-glibc-2.10.patch
+ epatch "${FILESDIR}"/wise-2.4.1-cflags.patch
+ epatch "${FILESDIR}"/01_welcome-csh.patch
+ epatch "${FILESDIR}"/02_isnumber.patch
+ epatch "${FILESDIR}"/03_doc-nodycache.patch
+ epatch "${FILESDIR}"/04_wise2-pdflatex-update.patch
+ # the two below are already in wise-2.2.0-glibc-2.10.patch
wise-2.4.1-cflags.patch
+ #epatch "${FILESDIR}"/06_getline.patch
+ #epatch "${FILESDIR}"/07_ld--as-needed.patch
+ epatch "${FILESDIR}"/08_mayhem.patch
+ epatch "${FILESDIR}"/09_dnal-add-return-statement.patch
+ epatch "${FILESDIR}"/11_consistent_manual_dates.patch
# cd "${S}"/docs || die
# cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl
> temp.tex || die
# cat wise2api.tex temp.tex apiend.tex > api.tex || die
# epatch "${FILESDIR}"/${PN}-api.tex.patch
-#}
+ #
+ # eventually, zap bundled but modified version of hmmer-2?
+ # This is not recommended, because sean and I diverged a while back on
indexing
+ # strategies. At some point I will need to port the later HMMer into
Wise2.
+ # rm -rf src/HMMer2 || die "Cannot zap bundled hmmer-2 sources"
+ # sed -e "s#HMMER_INCLUDE = ../HMMer2/#HMMER_INCLUDE =
${EPREFIX}/usr/include/hmmer2#" -i src/makefile || die
+ # sed -e "s#HMMER_LIBS.* = ../HMMer2/#HMMER_LIBS =
${EPREFIX}/usr/$(get_libdir)"#" -i src/makefile || die
+ # TODO: change eventual callers of the hmmer-2 binaries?
+ # ./test_data/*.{HMM,hmm}
+ # ./src/test/*.{HMM,hmm}
+ # ./src/perl/makelib.pl
+ #for e in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmpfam
hmmsearch; do \
+ # # append '2' to the filename in "$e"
+ #done
+}
src_compile() {
emake \
