problem with wildcard in emboss applications.

[Ted Chiang]

We are trying to iron out some issues in installing EMBOSS 2.1.0 and in
the email attached below, Len has described what he did to modify if for
IRIX.  

The applications are up and running, however I noticed that certain
applications do not take the 'wildcard' variable when retrieving
multiple database files as in EMBOSS 1.13.1.  

Here is an example using seqret (the problem also applies to the program
'stssearch'):

bash%seqret gbbct:*
Reads and writes (returns) sequences
Error: Unable to read sequence 'gbbct:*'


-->Has anyone seen this before? or have any suggestions?  (just as aside:
seqret and other applications works fine when retrieving only a single
database entry).


thanks.

-Ted


=====================================
Ted Chiang
Bioinformatics Supercomputing Centre
Hospital for Sick Children, Toronto
ext. 7028
tchiang at bioinfo.sickkids.on.ca









-------- Original Message --------
Subject: Emboss 2.1.0 on Irix
Date: Thu, 03 Jan 2002 10:41:28 -0500
From: Len Zaifman <leonardz at bioinfo.sickkids.on.ca>
To: Emboss Developer <emboss-dev at hgmp.mrc.ac.uk>

I have just built the emboss 2.1.0 suite on our Origin 3000. 

A couple of extra things were necessary because configure didn't quite
get it right. 

First off, I had always built previous emboss versions static because of
an error in configure. Due to an upgrade in our MipsPro compilers
(MisPRO 7.3.1.3m) , we can no longer build static. So I solved the
problem using sed on the Makefiles. Here are the relevant lines:

###
### This fixes the problem of building emboss shared
### Irix Compilers previous to MipsPRO 7.3.1.3m allowed static builds
### MipsPRO 7.3.1.3m and beyond do not. This fix was required to build
shared
###
f='plplot/Makefile'
sed -e 's/libplplot_la_LDFLAGS = -version-info
4:99:0/libplplot_la_LDFLAGS = /' $f > ${f}.new
mv ${f}.new $f
grep version $f
echo "$f fixed"


In otherwords, I needed to remove -version-info 4:99:0 . I am not sure
what effect this had to the resulting binaries. Hopefully, none. Please
let me know.

In addition, Configure puts in spurious -Lyes/lib lines in various
Makefiles

So : I also have the following:


###     Remove spurious yes/lib occurences
###
for f in ./ajax/Makefile ./nucleus/Makefile ./plplot/Makefile
./emboss/Makefile; do
        sed -e 's"\-Lyes/lib""' ${f} > ${f}.new
        mv ${f}.new $f
        grep -in 'yes/lib' $f
        echo "$f fixed"
done

I assume these have no effect as well on the resulting binaries.

Finally, in the Configure script, which appears below, I needed to set
several includes in the line setting the Compiler.  There were errors
when I put them in the CFLAGS variable. Has anyone else seen these
issues:

For specificity this is on an Origin 3000, Irix 6.5.14f, MipsPRO7.3.1.3m
compilers, and Java2 v1.3.1 Development Environment (Sun Java2 SDK
v1.3.1). 

The configure script

#! /usr/local/bin/bash
### 
### Set up to run in batch or interactively
###
#PBS -N CONFIGUREEMBOSS
#PBS -l cput=2:00:00
#PBS -l nodes=RED
export PATH=$PATH:/usr/local/bin:/usr/java/bin
export EMB_VER='2.1.0'
###
### set directory if in PBS
###
if [ $PBS_O_WORKDIR ] ; then
        cd $PBS_O_WORKDIR
fi
###
### set up to use Irix cc 
### for some reason putting  
###             -I/usr/local/include -I/usr/java/include
-I/usr/java/include/irix
### in CFLAGS does not work so I set them here in the CC definition
###
(date ; export CC="/usr/bin/cc  -I/usr/local/include -I/usr/java/include
-I/usr/java/include/irix"; \
export CFLAGS="-n32 -mips4 -Ofast"; \
export LD="/usr/bin/ld -n32 -mips4 -IPA -L/usr/local/lib32" ;echo " SGI
build for EMBOSS ${EMB_VER}  shared" ; \
./configure --srcdir=/src/emboss/${EMB_VER}/EMBOSS-${EMB_VER}
--prefix=/tools/emboss${EMB_VER}\
 --with-x --with-pngdriver --with-java  ; \
date ) 2>&1 | tee -a Configure.log
###
### fix makefile issues created by configure - don't know how to fix
configure
###
./fixit.sh 2>&1 | tee -a Configure.log
###
### make and install 
###
(date ; gmake ; date ; gmake install ; date ) 2>&1 | tee Make.log
echo "Done"