Overhaul packaging for new build system

README

MANUAL

Description: Append to CFLAGS and don't forcibly set CC

Author: Afif Elghraoui

Forwarded: no

Last-Update: 2015-10-30

--- trnascan-se.orig/Makefile

+++ trnascan-se/Makefile

@@ -33,11 +33,8 @@

 ## where you want temporary files stored

 TEMPDIR = /tmp

-## your compiler

-CC = gcc	  # GNU cc (if available) otherwise use vendor's cc

-

 ## any special compiler flags you want

-CFLAGS = -O    # ok for most machines (remove -O for DEC OSF/1 cc compiler)

+CFLAGS += -O    # ok for most machines (remove -O for DEC OSF/1 cc compiler)

 ## machine specific definitions

 #  You shouldn't need any. The specific #define's in squid are historical.

Description: Set install destination directories

Author: Afif Elghraoui <afif@ghraoui.name>

Forwarded: not-needed

Last-Update: 2015-10-30

--- trnascan-se.orig/Makefile

+++ trnascan-se/Makefile

@@ -20,9 +20,9 @@

 PERLBIN = perl

 ## where you want things installed

-BINDIR  = $(HOME)/bin

-LIBDIR  = $(HOME)/lib/tRNAscan-SE

-MANDIR  = $(HOME)/man

+BINDIR = $(DESTDIR)/usr/bin

+LIBDIR = $(DESTDIR)/usr/share/tRNAscan-SE

+MANDIR = $(DESTDIR)/usr/share/man

 ## NOTE !!  If you later manually move the location of 

 ## binaries or data files in the BINDIR or LIBDIR directories,

Description: Honor LDFLAGS in calls to CC

Author: Afif Elghraoui <afif@ghraoui.name>

Forwarded: no

Last-Update: 2015-10-30

--- trnascan-se.orig/Makefile

+++ trnascan-se/Makefile

@@ -107,17 +107,17 @@

 all: 	$(PROGS) tRNAscan-SE setpaths

 covels-SE:  $(OBJ) scan_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 coves-SE: $(OBJ) score_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o

 	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \

-	pavesi.o $(SQUIDOBJ) $(LIBS)

+	pavesi.o $(SQUIDOBJ) $(LIBS) $(LDFLAGS)

 trnascan-1.4: trnascan.o

-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c

+	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c $(LDFLAGS)

 tRNAscan-SE:

 	$(PERLDIR)/$(PERLBIN) checkversion.pl

@@ -199,12 +199,12 @@

 noambig: trnascan-1.4-NA eufindtRNA-NA

 trnascan-1.4-NA:  trnascan.o

-	$(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c

+	$(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c $(LDFLAGS)

 eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o

-	$(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 

+	$(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c $(LDFLAGS)

 	$(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \

-	pavesi-NA.o $(SQUIDOBJ) $(LIBS)	

+	pavesi-NA.o $(SQUIDOBJ) $(LIBS)	$(LDFLAGS)

 clean:

@@ -219,7 +219,7 @@

 	rmdir -ps $(MANDIR)

 .c.o:

-	$(CC) $(CFLAGS) $(MDEFS) -c $<		

+	$(CC) $(CFLAGS) $(MDEFS) -c $<	$(LDFLAGS)

 ## programs from Sean Eddy's sequence i/o function library not

 ## needed for tRNAscan-SE but included for their utility

@@ -232,16 +232,16 @@

 	cp $(UTILS) $(BINDIR)/.

 reformat: $(SQUIDOBJ) reformat_main.o

-	$(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)

+	$(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) $(LDFLAGS)

 revcomp: $(SQUIDOBJ) revcomp_main.o

-	$(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)

+	$(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) $(LDFLAGS)

 seqstat: $(SQUIDOBJ) seqstat_main.o

-	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)

+	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) $(LDFLAGS)

 shuffle: $(SQUIDOBJ) shuffle_main.o

-	$(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)

+	$(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) $(LDFLAGS)

 ## other programs in Cove package (below) not needed for

 ## tRNAscan-SE, but are included for users who wish to apply

@@ -254,25 +254,25 @@

 	cp $(COVE_SUITE) $(BINDIR)/.

 covea: $(OBJ) align_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 coveb: $(OBJ) build_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 covee: $(OBJ) emit_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 covet: $(OBJ) train_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 covels:  $(OBJ) scan_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 coves: $(OBJ) score_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 structcheck: $(OBJ) structcheck_main.o

-	$(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)

+	$(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) $(LDFLAGS)

 ## Maspar memory limits

Description: Fix warnings regarding tRNAscan-SE manpage

 Fix the "bad whatis entry" and "manpage has errors from man"

 lintian warnings. The latter was caused by quoted string at the beginning

 of the line that man apparently tried to interpret as a macro. That string

 was moved so that it wasn't at the beginning of the line anymore.

Author: Afif Elghraoui <afif@ghraoui.name>

Forwarded: no

Last-Update: 2015-10-30

--- trnascan-se.orig/tRNAscan-SE.man

+++ trnascan-se/tRNAscan-SE.man

@@ -1,11 +1,7 @@

 .TH "tRNAscan-SE" 1 "November 1997" "tRNAscan-SE 1.1"

 .SH NAME

-.TP

-.I tRNAscan-SE

-

-- a program for improved detection of transfer RNA genes 

-in genomic sequence

+tRNAscan-SE \- improved detection of transfer RNA genes in genomic sequence

 .SH SYNOPSIS

 .B tRNAscan-SE [options] seqfile(s)

 .SH DESCRIPTION

@@ -308,8 +304,8 @@

 translation table that is specified at the end of the tRNAscan-SE.src

 source file.  This option allows the user to specify exceptions to the

 default translation table.  The user may use any one of several

-alternate translation code files included in this package (see files

-'gcode.*'), or create a new alternate translation file.  See Manual

+alternate translation code files included in this package (see

+files 'gcode.*'), or create a new alternate translation file.  See Manual

 documentation for specification of file format, or refer to included

 examples files.  

 .sp 1