Problem with instalation Jemboss

Tarzan1984 · 11-01-2009, 02:52 PM

Hy.
I'm using MDV 2009.1. I've installed emboss v.5.0.0 from repo.
I've founded on homepage of emboss http://emboss.sourceforge.net/
this link for graphic gui http://emboss.sourceforge.net/Jemboss/.
Now I'm trying to install Jembos without effect :/
I've downloaded from this page http://emboss.sourceforge.net/Jemboss/ this gui. I've unpacked it with file-roller:

Code:

[tarzan@localhost Jemboss]$ ls
activation.jar         commons-logging.jar  JAE.bat                 jaxrpc.jar   JembossPrintAlignment.jar  runJAE       wsdl4j.jar
axis.jar               DNAed.bat            jakarta-regexp-1.2.jar  Jemboss.bat  mail.jar                   runJemboss*  xerces.jar
commons-discovery.jar  grout.jar            jalview.jar             Jemboss.jar  runDNAEd                   saaj.jar

and:

Code:

[tarzan@localhost Jemboss]$ java -jar Jemboss.jar
Failed to load Main-Class manifest attribute from
Jemboss.jar
[tarzan@localhost Jemboss]$ rumJemboss
bash: rumJemboss: command not found

I've read this http://emboss.sourceforge.net/Jembos...tandalone.html that I've to:

Quote:

Go to the directory where the script should be run from:

Code:

cd EMBOSS-3.x.x/jemboss/utils

I've tried to find it, but I can't:

Code:

[tarzan@localhost EMBOSS]$ ls
acd/  data/  doc/  emboss.default@  emboss.default.template  plstnd5.fnt  plxtnd5.fnt  test/

and:

Code:

[tarzan@localhost EMBOSS]$ locate install-jemboss-server.sh.
[tarzan@localhost EMBOSS]$ find install-jemboss-server.sh.
find: `install-jemboss-server.sh.': There is no such file or directory

Does anyone can help. Thank you for any advice

rolf · 11-01-2009, 06:30 PM

I don't know how the software is supposed to work but, just reading through your links:

@ http://emboss.sourceforge.net/Jembos...tandalone.html

Quote:

# Get the latest version of EMBOSS (which contains Jemboss)

ftp://emboss.open-bio.org/pub/EMBOSS/

Where I see

EMBOSS-latest.tar.gz 07/15/2009 10:47:00 AM

and, in that:

Code:

[rolf@localhost tarballs]$ tar tzvf EMBOSS-latest.tar.gz | grep install-jemboss-server.sh
-rwxr-xr-x 0/0           42752 2009-06-30 01:31 EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh

there is the script.

Tarzan1984 · 11-03-2009, 11:08 AM

Ok. I've installed from this server ftp ... Emboss-latest.tar.gz
But now. I have a second problem.
I can't still find this file install-jemboss-server.sh
This is what I've got after I've unpacked this .tar.gz:

Code:

[tarzan@localhost EMBOSS-6.1.0]$ ls
aclocal.m4     config.status*  emboss/      LICENSE      mkinstalldirs*  scripts/
ajax/          config.sub*     FAQ          ltmain.sh    NEWS            test/
AUTHORS        configure*      INSTALL      m4/          nucleus/        THANKS
ChangeLog      configure.in    install-sh*  Makefile     ONEWS
COMPAT         COPYING         jemboss/     Makefile.am  plplot/
config.guess*  depcomp*        KNOWN_BUGS   Makefile.in  PROBLEMS
config.log     doc/            libtool*     missing*     README

I've rad the Install file and:

Code:

./configure
make
make install

Everything is ok.
When I'm trying to run with:

Code:

[tarzan@localhost EMBOSS-6.1.0]$ cd /home/tarzan/Pobrane/EMBOSS-6.1.0 | ./runJemboss.sh
bash: ./runJemboss.sh: There is no such file or directory

I can't understand this ..
Help please

THX

rolf · 11-03-2009, 11:14 AM

Quote:

[rolf@localhost tarballs]$ tar tzvf EMBOSS-latest.tar.gz | grep install-jemboss-server.sh
-rwxr-xr-x 0/0 42752 2009-06-30 01:31 EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh

That shows you where the script is. cd there or give full path.

Tarzan1984 · 11-03-2009, 12:14 PM

Now next problem.
During the installation I've asked about:

Code:

Enter java (1.3 or above) location (/usr/java/jdk1.3.1/):

Where is it?? Because I can't anything like that :/
I've founded this:

Code:

java/                                       
java-1.4.0/                                       
java-1.4.1/                                     
java-1.4.2/                                   
java-1.5.0/                                       
java-1.6.0/                                   
java-1.7.0/

in /usr/share directory. But no sign of java v.1.3
What should I do now ??
Thx

knudfl · 11-03-2009, 01:15 PM

To know which java you have, if any,
please use this command :

java -version

The main location for java is /usr/lib/jvm/
and links to binaries in /usr/bin/
.. And you don't want java 1.3 .
.. The java, installed by default is OpenJDK-IcedTea,
which probably isn't usable for emboss.

The commands 1) su
2) urpmi java-1.6.0-sun
( or use the package manager )
.. will provide genuine java version 1.6.0_15 runtime.

3) update-alternatives --config java

Code:

There are 3 programs which provide `java'.

  Selection    Command
-----------------------------------------------
*+    1        /usr/lib/jvm/jre-1.6.0-openjdk/bin/java
      2        /usr/lib/jvm/jre-1.5.0-jamvm/bin/java
      3        /usr/lib/jvm/jre-1.6.0-sun/bin/java

Enter to keep the default[*], or type selection number: 3
Using `/usr/lib/jvm/jre-1.6.0-sun/bin/java' to provide `java'.

Please choose 3.
Emboss asking for java location, probably answer
/usr/lib/jvm/java-1.6.0-sun-1.6.0.15/
.....
.....
Emboss, fast download : http://ftp.sunet.se/pub/molbio/analyze/emboss/
.....

Tarzan1984 · 11-03-2009, 02:01 PM

Well

Code:

[root@localhost games]# java -version
java version "1.6.0_0"
OpenJDK Runtime Environment (IcedTea6 1.5) (mandriva-0.20.b16.0.3mdv2009.1-i386)
OpenJDK Server VM (build 14.0-b08, mixed mode)

And that's all I can get in console :/

Code:

[root@localhost utils]# ./install-jemboss-server.sh

--------------------------------------------------------------
         EMBOSS and Jemboss Server installation script        
--------------------------------------------------------------
                                                              
Note: any default values are given in square brackets [].     
                                                              
There are two types of installation see details at:           
http://emboss.sourceforge.net/Jemboss/install/setup.html      
                                                              
(1) CLIENT-SERVER                                             
(2) STANDALONE                                                
Enter type of installation [1] :                              
2                                                             






--------------------------------------------------------------
         EMBOSS and Jemboss Server installation script        
--------------------------------------------------------------

*** This script needs to be run with permissions to be able
*** to install EMBOSS in the required directories. This may
*** be best done as root or as a tomcat user.              

Before running this script you should download the latest:

(1) EMBOSS release (contains Jemboss) ftp://emboss.open-bio.org/pub/EMBOSS/

Has the above been downloaded (y/n)? 
y

Select the platform that your Jemboss server will be
run on from 1-8 [1]:
(1)  linux
(2)  aix
(3)  irix
(4)  hp-ux
(5)  solaris
(6)  macosX
(7)  OSF
(8)  FreeBSD
1

Enter java (1.4 or above) location [/usr]:
/usr/lib/jvm/java-1.6.0-sun-1.6.0.0
Enter java (1.3 or above) location (/usr/java/jdk1.3.1/):
/usr/lib/jvm/java-1.6.0-sun-1.6.0.0
Enter java (1.3 or above) location (/usr/java/jdk1.3.1/):

I don't get it really :/ I'm using mdv for 2 years, but now I've really stucked :/
Thx really for any advice

knudfl · 11-03-2009, 03:37 PM

1) First thing to do : # update-alternatives --config java
... Did you do that ? ? ?
You must of course install java-1.6.0-sun before you can choose it.

2) java -version
No " IcedTea6 " , please , 'java -version' must show :

java version "1.6.0_15"
Java(TM) SE Runtime Environment ...
.....
.....

3) The installer 'install-jemboss-server.sh' will accept this :
/usr/lib/jvm/java

.....

Tarzan1984 · 11-04-2009, 12:36 PM

Ok.
I've installed from repo package java-1.6.0-sun(JAva Runtime Environment for java-1.6.0-sun) version 1.6.0.15 but :

Code:

[root@localhost tarzan]# java -version
java version "1.6.0_0"
OpenJDK Runtime Environment (IcedTea6 1.5) (mandriva-0.20.b16.0.3mdv2009.1-i386)
OpenJDK Server VM (build 14.0-b08, mixed mode)

How can I get java version 1.6.0.15 ??
Thx for any help

rolf · 11-04-2009, 08:31 PM

Quote:

Originally Posted by knudfl

1) First thing to do : # update-alternatives --config java
... Did you do that ? ? ?
You must of course install java-1.6.0-sun before you can choose it.

[..]
.....

This reminder will be the third time this direction was given, at least. In Mandriva, when various installed programs provide the same thing, update-alternatives as root provides a way to set the default such program.

Tarzan1984 · 11-14-2009, 12:32 PM

Hi

What should I choose??:

Code:

[root@localhost tarzan]# update-alternatives
update-alternatives: need --display, --config, --set, --install, --remove, --remove-all, --list or --auto

Mandriva update-alternatives 1.9.0, derived from the Debian GNU/Linux
update-alternatives tool, which is Copyright (C) 1995 Ian Jackson. This is
free software; see the GNU General Public Licence version 2 or later for
copying conditions.  There is NO warranty.

Usage: /usr/sbin/update-alternatives [<option> ...] <command>

Commands:
  --install <link> <name> <path> <priority>
    [--slave <link> <name> <path>] ...
                           add a group of alternatives to the system.
  --remove <name> <path>   remove <path> from the <name> group alternative.
  --remove-all <name>      remove <name> group from the alternatives system.
  --auto <name>            switch the master link <name> to automatic mode.
  --display <name>         display information about the <name> group.
  --list <name>            display all targets of the <name> group.
  --config <name>          show alternatives for the <name> group and ask the
                           user to select which one to use.
  --set <name> <path>      set <path> as alternative for <name>.

<link> is the symlink pointing to /etc/alternatives/<name>.
<name> is the master name for this link group.
<path> is the location of one of the alternative target files.
<priority> is an integer; options with higher numbers have higher priority in
  automatic mode.

Options:
  --altdir <directory>     change the alternatives directory.
  --admindir <directory>   change the administrative directory.
  --verbose                verbose operation, more output.
  --quiet                  quiet operation, minimal output.
  --help                   show this help message.
  --version                show the version.

Thx for any help

rolf · 11-14-2009, 07:30 PM

update-alternatives --config java

Really, this is the fourth time the command has been written and you can't see that? It's irritating to spend time not to have someone make the effort, apparently, to simply read. Or, are you a troll?

update-alternatives --config java

copy/paste that after the root prompt. Press Return. Choose the number for the appropriate java and press Return.

Tarzan1984 · 01-16-2010, 05:07 AM

Sorry, I'm sometimes doing stuppid misteakes :/
Thx for advices. In future I will read instructions better