SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bioo Scientific is Launching NEXTflex-96™ DNA Barcodes to Significantly Increase NGS Bioo Scientific Vendor Forum 0 09-29-2011 12:11 PM
Installing Roche 454 Analysis software version 2.6 (gsAssembler) on Fedora 15 dsenalik 454 Pyrosequencing 1 09-27-2011 06:29 AM
BWA crashes in Fedora ulz_peter Bioinformatics 4 05-09-2011 04:04 AM
bfast match problem on fedora 14 sammy07 Bioinformatics 5 02-08-2011 08:24 AM
454 and cluster operating systems - patching Fedora rglover 454 Pyrosequencing 3 05-20-2010 06:23 AM

Reply
 
Thread Tools
Old 01-15-2009, 09:31 AM   #1
cbean127
Junior Member
 
Location: CT

Join Date: Jan 2009
Posts: 2
Default launching gsAssembler in Fedora

I have installed the off-rig Application software on a computer running RedHat 5 and have had no problems launching the gsAssembler from the command line. I have just installed the off-rig software on a machine running Fedora 10 and I cannot launch the gsAssembler application. It seems to be an issue with Java. Has anyone had this problem? Is anyone running the off-rig software on a non-Redhat machine?
cbean127 is offline   Reply With Quote
Old 01-16-2009, 02:32 AM   #2
Raj
Member
 
Location: UK

Join Date: Jan 2009
Posts: 15
Default

Hi,
I had a similar problem using fedora, the way i got it to work was to, set a couple of paths to the software, depending on what version you are using the paths will be different.

Version 1.X

Assuming you've installed it the way the install files says to do it, specifically you've setup the /usr/local/rig directory.

At the linux prompt, i'm using the bash shell, type:
>PATH=$PATH:/usr/local/rig/bin
>RIGDIR=/usr/local/rig
>export PATH
>export RIGDIR
>gsAssembler or any other program

Version 2.X
You need to set the path to where the 454 directory was created/installed, so in my case, i installed it in my home directory.

NB. The Bash shell was used...

>export PATH=$PATH:/home/Raju/454/bin
>gsAssembler or any other program
Raj is offline   Reply With Quote
Old 01-16-2009, 05:47 AM   #3
cbean127
Junior Member
 
Location: CT

Join Date: Jan 2009
Posts: 2
Default

Thanks Raj but I have already added the path to the bash_profile. My problem seems to be an issue with java. When I attempt to launch the gsAssembler command I get the following error:

/home/imac/454/apps/assembly/bin/gsAssembler: line 124: /home/imac/454/apps/assembly//jre/jre1.5.0_07/bin/java: cannot execute binary file

I am stuck at this point.
cbean127 is offline   Reply With Quote
Old 01-16-2009, 07:51 AM   #4
Raj
Member
 
Location: UK

Join Date: Jan 2009
Posts: 15
Default

I'm also using Fedora 10, in the 454 directory, if i run the application e.g. gsMapper from the directory 454/bin the GUI boots up.

If i go to via the apps directory, I get the command line version.

I used to get the java error in earlier versions of offinst., but i found that the software couldn't find the appropriate directories, hence the setting the paths specifically as well ensuring i had full permissions when i did the install i.e. >sudo ./INSTALL

I'm guessing your running version 2.X, which shouldn't be a problem in fedora. I didn't get the java error, in version 2... all i did, was go to my home dir, unzipped/tar the program and install.

If i think of anything else.. i'll post it here....
Raj is offline   Reply With Quote
Old 02-02-2009, 06:11 AM   #5
coldturkey
Member
 
Location: Brisbane

Join Date: Nov 2008
Posts: 51
Default

I have a slightly different problem when trying to run gs Assembler on Ubuntu. I get the following error

path/apps/assembly/bin/gsAssembler: 114: Syntax error: "(" unexpected

any ideas?
coldturkey is offline   Reply With Quote
Old 03-09-2009, 07:51 AM   #6
torbean
Member
 
Location: EMEA

Join Date: Feb 2009
Posts: 11
Default

Hi to all. I have the same problem now and have no idea how to overcome it. Fedora 10, 32x, Roche soft 2.X version installed under root. I can launch gsAssembler, but can´t start the run. Error: /opt/454/bin/createProject: cannot execute binary file
I added path already... Installed java
Can anyone help, please?
torbean is offline   Reply With Quote
Old 03-16-2009, 05:21 AM   #7
Emanuel Heitlinger
Member
 
Location: Karlsruhe

Join Date: Mar 2009
Posts: 11
Default Syntax error: "(" unexpected

Same Problem as coldturkey
/opt/454/apps/assembly/bin/gsAssembler: 114: Syntax error: "(" unexpected

Most likely reason:
On Ubuntu the .rpm files are not installed! The GUI needs some of them. I will just stick to the command line version... But there is also a tool to convert .rpm to something ubuntu can use.
Emanuel Heitlinger is offline   Reply With Quote
Old 03-16-2009, 09:11 AM   #8
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Since that part of the code pertains to finding jre1 and then setting a variable to the found location, I suggest just hard-coding the location into the code. You may be running into problems with incompatible shells or even 'find' commands.
westerman is offline   Reply With Quote
Old 08-17-2009, 11:51 AM   #9
hengnck
Junior Member
 
Location: New Zealand

Join Date: Aug 2009
Posts: 9
Default GS Assembler on Fedora

Hi All,
The GS FLX software versions 1 and 2 will work on Fedora 10 and 11 but *only* with the 32-bit version using the standard bash.rc entries, i.e., export rigdir and export path. I presume that you've set up the 64-bit version.

A better alternative is CentOS, both 32- and 64-bit versions - CentOS is currently at version 5.3.

Note of caution: In my experience, doing GS assemblies on different Red Hat lineage systems will differ even with the *same data set*! For example, Fedora 10 generated 148 contigs, Fedora 11 (148), CentOS 5.2 (149) - all with the same data set and parameters. The missing contig appeared to be a misassembly.

Bottom line: Whatever system you are working with, stick to the data you obtain because you may not repeat elsewhere.

Disclaimer: I'm not a Linux guru (not by any stretch of the imagination), but I've spent a considerable amount of time trying to get the GS software working. No, it does not work on systems of Debian lineage - generates the syntax error - the problem is in the run script, I think.
hengnck is offline   Reply With Quote
Old 02-24-2010, 06:03 AM   #10
palmeira
Junior Member
 
Location: Liege/Luik/Luttich @ Belgium

Join Date: Feb 2010
Posts: 1
Default Syntax error: "(" unexpected [Debian and Ubuntu]

Hello everyone,

a very simple fix to the following error:

Syntax error: "(" unexpected

change the first line of the two following files from #!/bin/sh to #!/bin/bash (or any other path to your bash interpreter):

$rootdir/apps/assembly/bin/gsAssembler
$rootdir/apps/mapper/bin/gsMapper

This will get the GUI of both gsMapper and gsAssembler to work smoothly on Debian/Ubuntu systems (possibly also on other systems presenting the [Syntax error: "(" unexpected] error at launching).

Cheers,
Leo.
palmeira is offline   Reply With Quote
Old 02-25-2010, 11:59 AM   #11
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

The roche software is really funny, ... using jar,rpm,tar.gz for installations, alle mixed, suppressing any erros and the scripts are really, hmmm, ugly?

I have "successfully" installed the off-rig software on our home-made linux system; there
was not one binary installed :-) They use very funny ways extracting RPMs for installation ... and change these methods from time to time ..

sigh,
Sven
sklages is offline   Reply With Quote
Old 03-03-2010, 03:06 PM   #12
ajthomas
Senior Member
 
Location: Utah

Join Date: Mar 2010
Posts: 162
Default

Quote:
Originally Posted by hengnck View Post
Hi All,
The GS FLX software versions 1 and 2 will work on Fedora 10 and 11 but *only* with the 32-bit version using the standard bash.rc entries, i.e., export rigdir and export path. I presume that you've set up the 64-bit version.

A better alternative is CentOS, both 32- and 64-bit versions - CentOS is currently at version 5.3.
I tried CentOS, but had the same problems that I did with Red Hat--video drivers didn't work properly, wireless didn't work, couldn't mount NTFS partition, etc.--so I installed Fedora 11. The FLX software ran fine under the 32-bit version, but not 64-bit. The problem is that Java is in a different place under 64-bit, and the FLX software looks for Java where it is in the 32-bit version. I did a bit of research on my own and got half-way there, then the tech support people sent me this solution:
Quote:
install the GS FLX 2.0.01 64 Bit off-instrument software and then

sudo yum install zlib.i386 libXi.i386 libXtst.i386 libXaw.i386

this will install the necessary 32-bit options
I had to change the .i386 to .i586 to get it to work, but in the end it worked just fine.
ajthomas is offline   Reply With Quote
Old 11-09-2010, 04:53 AM   #13
Raiu
Junior Member
 
Location: Clemson, SC

Join Date: Nov 2010
Posts: 1
Default Another question about installing gsAssembler on Ubuntu

Quote:
Originally Posted by palmeira View Post
Hello everyone,

a very simple fix to the following error:

Syntax error: "(" unexpected

change the first line of the two following files from #!/bin/sh to #!/bin/bash (or any other path to your bash interpreter):

$rootdir/apps/assembly/bin/gsAssembler
$rootdir/apps/mapper/bin/gsMapper

This will get the GUI of both gsMapper and gsAssembler to work smoothly on Debian/Ubuntu systems (possibly also on other systems presenting the [Syntax error: "(" unexpected] error at launching).

Cheers,
Leo.
Sorry to bring this thread back from the dead, but I was wondering if anyone would have an answer to a question related to this.
I am trying to install gsAssembler on Ubuntu. After installing with sudo rights to opt/454 I got the error described above. Then I made the change Leo suggested (bin/sh --> bin/bash) and that fixed the error
BUT
Now when gsAssembler loads the GUI is blank. I mean, I can see the window but none of the icons are visible, I think they are there because if I move my mouse pointer around it changes from arrow to hand at certain places. But I can't see what I'm clicking.
I tried using alien to install the rpm files on my installation cd and was able to install all but one. gsSupportTool-1.16.02-1.i386.rpm would not extract and install. Installing the other rpm files did not fix the blank GUI.
Any help would really be appreciated!
Raiu is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO