The myemboss package is an almost empty EMBASSY package where developers can safely build their own EMBOSS applications. It provides a way to isolate local application development from the rest of EMBOSS so preserving the integrity of the package. New applications, regardless of whether they are destined for another EMBASSY package or EMBOSS itself, will typically start their life in myemboss.

myemboss requires the GNU tools autoconf, automake and libtool to be installed (see Section 1.2, “Installation of CVS (Developers) Release”). Using the GNU tools you can add new applications very easily. myemboss provides a directory structure and Makefile stubs for integrating new applications. Application ACD files go in the myemboss/emboss_acd directory and source code into the myemboss/src directory.

Applications are built using a Makefile file, but you do not need to edit this file directly. Instead you edit a file Makefile.am which automake converts into a file Makefile.in and configure converts into the Makefile file.

The Makefile.am file is shown below and has been edited to include two applications:

#

SUBDIRS = source emboss_acd emboss_doc

EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess

# tar to pick up the other directories
# then remove any CVS subdirectories

dist-hook:
	tar cBf - emboss_acd | ( cd $(distdir); tar xBf - ; cd emboss_acd; rm -rf CVS) 
	tar cBf - emboss_doc | ( cd $(distdir); tar xBf - ; cd emboss_doc; rm -rf CVS; rm -rf master) 

To compile applications in myemboss, you must configure the package if you have not already done so (see Section 1.2, “Installation of CVS (Developers) Release”), then type the following from the myemboss applications directory (myemboss/src):

make will regenerate the Makefile file and build your new application, linking it to the EMBOSS libraries (AJAX and NUCLEUS).

This assumes you have installed and configured EMBOSS and the myemboss package. If you did a full EMBOSS install using make install then you must also type:

to complete the installation of applications developed under myemboss.

For more information on installation see Section 1.2, “Installation of CVS (Developers) Release” and the EMBOSS Administrators Guide.

An application that has been developed and tested in myemboss can be added to the main package. Adding new applications to EMBOSS is essentially the same as for myemboss. EMBOSS has its own Makefile.am which, in contrast to myemboss, organises applications into two strands:

Applications which are not entirely complete should be put into the "make check" area of the emboss/Makefile.am file. For example, applications which compile and work correctly, but for which full documentation and quality assurance tests are not yet available, should go here. Only applications which are fully working, tested and documented should go into the "make" area.

An excerpt from the Makefile.am file is below and includes a few "make check" applications and standard "make" applications:

SUBDIRS = acd data

EXTRA_DIST = emboss.default.template

if ISSHARED
if ISAIXIA64
AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../ajax/.libs -lajax
else
AM_CFLAGS =
endif
endif


check_PROGRAMS = acdlog acdxsd ajtest \
complex corbatest \
entrails entrailsbook entrailshtml entrailswiki giep histogramtest intconv \
origsplitter origunion \
newcoils \
... <lines omitted for brevity> 


bin_PROGRAMS = aaindexextract abiview \
acdc acdpretty acdtable acdtrace acdvalid \
aligncopy aligncopypair antigenic \
backtranambig backtranseq banana biosed btwisted \
... <lines omitted for brevity> 

water whichdb wobble \
wordcount wordfinder wordmatch wossname \
yank

INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax -I$(top_srcdir)/plplot

aaindexextract_SOURCES = aaindexextract.c
abiview_SOURCES = abiview.c
acdc_SOURCES = acdc.c
acdpretty_SOURCES = acdpretty.c
acdtable_SOURCES = acdtable.c

... <lines omitted for brevity> 

seqretsingle_SOURCES = seqretsingle.c
seqrettype_SOURCES = seqrettype.c
testplot_SOURCES = testplot.c
treetypedisplay_SOURCES = treetypedisplay.c

# Uncomment to use dual libraries
if ISCYGWIN
LDADD = ../nucleus/libnucleus.la ../ajax/libajax.la ../plplot/libeplplot.la $(XLIB)
else
LDADD = ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la $(XLIB)
endif

pkgdata_DATA = emboss.default.template
pkgdatadir=$(prefix)/share/$(PACKAGE)

#if PURIFY
#  LINK = purify $(LIBTOOL) --mode=link $(CC) $(CFLAGS) $(LDFLAGS) -o $@
#else
#
#endif

Compilation is the same as for myemboss. You must configure the EMBOSS package if you have not already done so (see Section 1.2, “Installation of CVS (Developers) Release”), then from the applications directory (e.g. /home/auser/emboss/emboss/emboss/) type:

This will regenerate the Makefile file, build your new application and link it to the libraries. If you installed EMBOSS using make install then you must also type:

to complete the installation of the new application.

For more information on installation see Section 1.2, “Installation of CVS (Developers) Release” the EMBOSS Administrators Guide.

Applications are added to EMBASSY packages in exactly the same way as for myemboss (see above).

To add an entirely new EMBASSY package you must:

% cd emboss/emboss/embassy/hmmernew/
% ls
AUTHORS       COPYING  emboss_acd  ltmain.sh    NEWS    Userguide.pdf
ChangeLog     CVS      emboss_doc  m4           README
configure.in  DOCS     INSTALL     Makefile.am  src

#

SUBDIRS = source emboss_acd emboss_doc

EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess

# tar to pick up the other directories
# then remove any CVS subdirectories

dist-hook:
	tar cBf - emboss_acd | ( cd $(distdir); tar xBf - ; cd emboss_acd; rm -rf CVS) 
	tar cBf - emboss_doc | ( cd $(distdir); tar xBf - ; cd emboss_doc; rm -rf CVS; rm -rf master) 

## Process this file with automake to produce Makefile.in

EXTRA_DIST = Makefile.am

bin_PROGRAMS = myseq mytest

if LOCALLINK
INCLUDES = -I../include -I../../../nucleus -I../../../ajax -I../../../plplot
else
INCLUDES = -I../include -I${embprefix}/include -I${embprefix}/include/eplplot
endif


if ISSHARED
if ISAIXIA64
if LOCALLINK
AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../plplot/.libs -L../../../ajax/.libs -L../../../nucleus/.libs -lnucleus -lajax -leplplot
else
AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lajax -leplplot
endif
else
AM_CFLAGS =
endif
endif


myseq_SOURCES = myseq.c
mytest_SOURCES = mytest.c



if LOCALLINK
LDADD = ../../../nucleus/libnucleus.la ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libeplplot.la $(XLIB)
else
LDADD = -L${embprefix}/lib -lnucleus -lajaxg -lajax -leplplot $(XLIB)
endif

EXTRA_DIST = Makefile.am

pkgdata_DATA = myseq.acd mytest.acd

pkgdatadir=$(prefix)/share/EMBOSS/acd

SUBDIRS = html text

pkgdata_DATA = index.html \
	myseq.html

pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/myseq

pkgdata_DATA =  myseq.txt

pkgdatadir=$(prefix)/share/EMBOSS/doc/programs/text

Any new functions and datatypes added to AJAX or NUCLEUS should be properly documented (Appendix D, Code Documentation Standards) if they are to be incorporated into the EMBOSS distribution. To compile the new code, type:

from the AJAX or NUCLEUS directory as appropriate. Of course, you will need to recompile any statically linked applications to use the changes. Alternatively, recompile the whole package by typing make from the second level EMBOSS directory e.g.:

If you have added entirely new library files then these must be integrated into AJAX or NUCLEUS by editing the Makefile.am in the AJAX or NUCLEUS directory as appropriate.

An excerpts of the the AJAX Makefile.am file:

## Process this file with automake to produce Makefile.in

if ISCYGWIN
lib_LTLIBRARIES = libajax.la
else
lib_LTLIBRARIES = libajax.la libajaxg.la
endif

if ISSHARED
if ISAIXIA64
if NEEDAJAX
AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
else
AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
endif
else
AM_CFLAGS =
endif
endif

if ISCYGWIN
AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
endif

## PCRE stuff (version 4.3)

POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@
PCRELIBVERSION = @PCRE_LIB_VERSION@
PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@

INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) -DPREFIX=\"$(prefix)\" -I$(top_srcdir)/plplot $(POSIX_MALLOC_THRESHOLD) 
#LDFLAGS = -no-undefined
LIBS =

AJAXSRC = ajacd.c ajalign.c ajarr.c ajassert.c \
ajbase.c \
ajcall.c ajcod.c \
ajdan.c ajdmx.c ajdom.c ajdomain.c ajexcept.c \
ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajindex.c ajjava.c ajlist.c \
ajmath.c ajmatrices.c ajmem.c ajmess.c ajnam.c ajnexus.c \
ajpat.c ajpdb.c ajpdbio.c ajphylo.c \
ajrange.c ajreg.c ajreport.c \
ajseq.c ajseqabi.c ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c \
ajsort.c ajstr.c ajsys.c \
ajtable.c ajtime.c ajtranslate.c ajtree.c ajutil.c ajvector.c \
pcre.c pcre_study.c pcreposix.c

AJAXGSRC = ajgraph.c ajhist.c

include_HEADERS = ajax.h ajarch.h ajdefine.h \
ajacd.h ajalign.h ajarr.h ajassert.h \
ajbase.h ajcall.h ajcod.h \
ajdan.h ajdmx.h ajdom.h ajdomain.h ajexcept.h \
ajfeat.h ajfeatdata.h ajfile.h ajfmt.h \
ajgraph.h ajgraphxml.h ajgraphstruct.h ajhist.h ajindex.h ajjava.h ajlist.h \
ajmath.h ajmatrices.h ajmem.h ajmess.h ajnam.h ajnexus.h \
ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
ajrange.h ajreg.h ajreport.h \
ajseq.h ajseqabi.h ajseqdata.h ajseqdb.h ajseqread.h ajseqtype.h ajseqwrite.h \
ajsort.h ajstr.h ajsys.h \
ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h \
pcre.h pcre_chartables.c pcre_config.h pcre_get.c pcre_printint.c \
pcre_internal.h pcreposix.h


if ISCYGWIN
libajax_la_SOURCES = $(AJAXSRC) $(AJAXGSRC)
libajax_la_LDFLAGS = -version-info 5:0:0
else
libajax_la_SOURCES = $(AJAXSRC)
libajax_la_LDFLAGS = -version-info 5:0:0
libajaxg_la_SOURCES = $(AJAXGSRC)
libajaxg_la_LDFLAGS = -version-info 5:0:0
endif

The NUCLEUS Makefile.am file:

## Process this file with automake to produce Makefile.in

lib_LTLIBRARIES = libnucleus.la

if ISSHARED
if ISAIXIA64
AM_CFLAGS = -Wl,-G -lm -L../ajax/.libs -lajax
else
AM_CFLAGS =
endif
endif

if ISCYGWIN
AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -L../ajax -leplplot -lajax
endif


INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ -I$(top_srcdir)/ajax

LIBS =

NUCLSRC =  embaln.c embcom.c embcons.c \
	   embdata.c embdbi.c embdmx.c embdomain.c \
	   embest.c embexit.c embgroup.c \
	   embiep.c embindex.c embinit.c \
	   embmat.c embmisc.c embmol.c \
	   embnmer.c embpat.c embpatlist.c embprop.c embpdb.c \
           embread.c embsig.c \
	   embshow.c embword.c

libnucleus_la_SOURCES = $(NUCLSRC)

libnucleus_la_LDFLAGS =  -version-info 5:0:0

include_HEADERS = emboss.h \
		 embaln.h embcom.h embcons.h \
		 embdata.h embdbi.h embdmx.h embdomain.h \
		 embest.h embexit.h embgroup.h \
		 embiep.h embindex.h embinit.h \
		 embmat.h embmisc.h embmol.h \
		 embnmer.h embpat.h embpatlist.h embprop.h embpdb.h \
                 embread.h embsig.h \
                 embshow.h embword.h 

You must also add any new header files to ajax.h and / or emboss.h. ajax.h looks like this:

#ifdef __cplusplus
extern "C"
{
#endif

/*
**
** AJAX master include file
**
*/

#ifndef ajax_h
#define ajax_h

#include <stdio.h>

#include "ajarch.h"

#include <stdarg.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/*#include <malloc.h>*/

#include "ajassert.h"
#include "ajdefine.h"
#include "ajstr.h"
#include "ajtime.h"
#include "ajfile.h"
#include "ajlist.h"

#include "ajtable.h"
#include "ajnexus.h"
#include "ajfeat.h"
#include "ajseq.h"
#include "ajseqdata.h"
#include "ajseqtype.h"
#include "ajarr.h"
#include "ajseqread.h"
#include "ajseqwrite.h"
#include "ajindex.h"
#include "ajseqdb.h"
#include "ajseqabi.h"
#include "ajreport.h"
#include "ajfmt.h"
#include "ajmatrices.h"
#include "ajalign.h"

#include "ajrange.h"
#include "ajcod.h"
#include "ajmath.h"

...
... Entries omitted for brevity
...

#endif

#ifdef __cplusplus
}
#endif

emboss.h looks like this:

#ifndef emboss_h
#define emboss_h

#include "ajax.h"
#include "ajgraph.h"
#include "embaln.h"
#include "embcom.h"
#include "embcons.h"
#include "embdbi.h"
...
... Entries omitted for brevity
...

#ifdef WIN32
#define VERSION "5.0.0"
#endif


#endif