EMBOSS

I made a stab at building EMBOSS but failed and succeeded, I think.

According to the adminguide, it requires zlib and libpng as well as gd. Since EMBOSS is set up for Linux, I will probably have to edit the config file to show where these libraries are on my machine.

I installed zlib and libpng to get matplotlib up and running (according to Gavin Huttley's wiki instructions).

Let's get gd. Downloaded gd-2.0.35.tar.gz from this page. According to the readme, it's the usual:

./configure make install

(using sudo). And it has a problem:

gdft.c:1403:35: error: fontconfig/fontconfig.h: No such file or directory gdft.c:1466: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token gdft.c:1479: error: expected ')' before '*' token gdft.c: In function 'font_pattern': gdft.c:1516: error: 'FcPattern' undeclared (first use in this function) gdft.c:1516: error: (Each undeclared identifier is reported only once gdft.c:1516: error: for each function it appears in.) gdft.c:1516: error: 'font' undeclared (first use in this function) gdft.c:1517: error: 'FcChar8' undeclared (first use in this function) gdft.c:1517: error: 'file' undeclared (first use in this function) gdft.c:1518: error: 'pattern' undeclared (first use in this function) gdft.c:1525: warning: assignment makes pointer from integer without a cast gdft.c:1531: error: expected ')' before 'FcChar8' gdft.c:1538: error: 'FC_FILE' undeclared (first use in this function) gdft.c:1538: error: 'FcResultMatch' undeclared (first use in this function) make[1]: *** [gdft.lo] Error 1 make: *** [install-recursive] Error 1

It seems to be related to a library called Fontconfig.

Get fontconfig-2.8.0.tar.bz2 from here. According to INSTALL do:

./configure --sysconfdir=/etc --prefix=/usr --mandir=/usr/share/man

but it fails because there is no configure, why not? From a web search it seems that

autoconf processes configure.in to produce a configure script

so I try this:

$ autoconf configure.in:36: error: possibly undefined macro: AM_INIT_AUTOMAKE If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. configure.in:38: error: possibly undefined macro: AM_MAINTAINER_MODE configure.in:59: error: possibly undefined macro: AM_CONFIG_HEADER configure.in:64: error: possibly undefined macro: AC_LIBTOOL_WIN32_DLL configure.in:65: error: possibly undefined macro: AM_PROG_LIBTOOL configure.in:78: error: possibly undefined macro: AM_CONDITIONAL

and then do as before:

$ sudo ./configure --sysconfdir=/etc --prefix=/usr --mandir=/usr/share/man ./configure: line 1728: syntax error near unexpected token `fontconfig,' ./configure: line 1728: `AM_INIT_AUTOMAKE(fontconfig, 2.8.0)'

It looks like I'm supposed to use autoconf, but first I have to fix the above error.

After another web search, try adding this to configure.in

m4_pattern_allow([AM_INIT_AUTOMAKE]) m4_pattern_allow([AM_MAINTAINER_MODE]) m4_pattern_allow([AM_CONFIG_HEADER]) m4_pattern_allow([AC_LIBTOOL_WIN32_DLL]) m4_pattern_allow([AM_PROG_LIBTOOL]) m4_pattern_allow([AM_CONDITIONAL])

autoconf goes fine. Now:

$ sudo ./configure --sysconfdir=/etc --prefix=/usr --mandir=/usr/share/man ./configure: line 1736: syntax error near unexpected token `fontconfig,' ./configure: line 1736: `AM_INIT_AUTOMAKE(fontconfig, 2.8.0)'

And I'm stuck. You can't feed fontconfig to AM_INIT_AUTOMAKE.No EMBOSS for me, it seems.

[UPDATE: I found instructions for installing GD here. It turns out I already had /usr/X11R6/include/fontconfig. The test of GD looks fine.

Followed simple instructions for EMBOSS and did:

./configure make make install

And after searching around for 10 minutes I finally ran:

/usr/local/share/EMBOSS/jemboss/runJemboss.sh

Now I have a window to play with (graphic at top of post)! ]