SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Newbler 2.7 on BioLinux 7.0 (Ubuntu 12.04.1 LTS) cement_head 454 Pyrosequencing 14 06-05-2015 06:28 AM
Installing Newbler 2.7 on Ubuntu 12.04, java problem JackieBadger Bioinformatics 22 05-14-2013 06:17 AM
Installing Newbler 2.5.3 on 64 bit Ubuntu...anyone??? WaltL 454 Pyrosequencing 30 10-31-2011 12:06 AM
Newbler 2.5.3 (gsAssembler) on Ubuntu or Rocks cluster? biojen 454 Pyrosequencing 0 03-01-2011 05:15 PM
Newbler 2.3 on Ubuntu- Anyone? WaltL 454 Pyrosequencing 2 12-03-2010 11:16 AM

Reply
 
Thread Tools
Old 08-12-2013, 05:51 PM   #1
brymerr921
Junior Member
 
Location: Utah

Join Date: Aug 2013
Posts: 4
Default Install Newbler 2.9 in Ubuntu

Hey everyone,

I am trying to install the Data_Analysis2.9 package in Ubuntu 13.04. I am very new to Ubuntu and Newbler, but am trying to get this to work.

Here is what I have done so far:
1. Download DataAnalysis_2.9_All_20130530_1559.tgz
2. Extract the *.tgz file to a folder on my desktop called "DataAnalysis_2.9_All"
3. Open terminal, and run
Code:
sudo apt-get install ia32-libs
4. From the bottom directory, type
PHP Code:
sudo ln -/bin/true /bin/rocks 
(sudo ln -s /bin/true ~/bin/rocks didn't work.)
5. Type
Code:
sudo apt-get install alien
6. Type
PHP Code:
ln -/bin/sh 
returns
PHP Code:
lrwxrwxrwx 1 root root 4 Aug 12 18:29 /bin/sh -> bash 
7. In /Desktop/DataAnalysis_2.9_All, type
PHP Code:
sudo ./setup.sh 
Then I get this error in the log file:
Code:
Installation started at 08/12/2013 06:45:41 PM

User: uid=0(root) gid=0(root) groups=0(root)

Hostname: bryan-ubuntu

=============================
[06:45:41 PM] cd /home/bryan/Desktop/DataAnalysis_2.9_All; md5sum -c checksum_inst

./setup.sh: OK
./README: OK
./packages/gsNewbler-2.9-1.x86_64.rpm: OK
./packages/amplicons_CLI_2.9.i686.tgz: OK
./packages/jre-linux-i586-oracle-2.9-1.i386.rpm: OK
./packages/gsNewbler-2.9-1.i686.rpm: OK
./packages/gsAssembler-2.9-1.noarch.rpm: OK
./packages/gsSeqTools-2.9-1.x86_64.rpm: OK
./packages/gsAmplicons-2.9-1.noarch.rpm: OK
./packages/gsSeqTools-2.9-1.i686.rpm: OK
./packages/gsMapper-2.9-1.noarch.rpm: OK
=============================

=============================
[06:45:42 PM] rpm -U   --force  /home/bryan/Desktop/DataAnalysis_2.9_All/packages/jre-linux-i586-oracle-2.9-1.i386.rpm

rpm: RPM should not be used directly install RPM packages, use Alien instead!
rpm: However assuming you know what you are doing...
warning: /home/bryan/Desktop/DataAnalysis_2.9_All/packages/jre-linux-i586-oracle-2.9-1.i386.rpm: Header V3 DSA/SHA1 Signature, key ID e50b562c: NOKEY
=============================

=============================
[06:45:44 PM] rpm -U   --force  /home/bryan/Desktop/DataAnalysis_2.9_All/packages/gsSeqTools-2.9-1.x86_64.rpm

rpm: RPM should not be used directly install RPM packages, use Alien instead!
rpm: However assuming you know what you are doing...
warning: /home/bryan/Desktop/DataAnalysis_2.9_All/packages/gsSeqTools-2.9-1.x86_64.rpm: Header V3 DSA/SHA1 Signature, key ID e50b562c: NOKEY
error: Failed dependencies:
	/bin/sh is needed by gsSeqTools-1:2.9-1.x86_64
=============================
This looks like the same error discussed at http://seqanswers.com/forums/showthread.php?t=20588, yet I can't get this to install. Thanks!
brymerr921 is offline   Reply With Quote
Old 08-12-2013, 06:31 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
Default

Did you try the code in post #5 from the thread that you have linked to? If you did then what do you see when you run the following?

Code:
$ ls -l /bin/sh
GenoMax is offline   Reply With Quote
Old 08-12-2013, 06:38 PM   #3
brymerr921
Junior Member
 
Location: Utah

Join Date: Aug 2013
Posts: 4
Default

I did the following commands:

[email protected]:~$ sudo rm /bin/sh
[sudo] password for bryan:
[email protected]:~$ sudo ln -s bash /bin/sh
[email protected]:~/Desktop/DataAnalysis_2.9_All$ ls -l /bin/sh
lrwxrwxrwx 1 root root 4 Aug 12 19:35 /bin/sh -> bash

I then tried to run setup.sh from Terminal and got the same error.
brymerr921 is offline   Reply With Quote
Old 08-12-2013, 06:52 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
Default

That looks right. I wonder if you have a problem with your $PATH variable (i.e. /bin is not in that path, it seems unlikely).

What is the output of

Code:
$ echo $PATH
GenoMax is offline   Reply With Quote
Old 08-12-2013, 06:56 PM   #5
brymerr921
Junior Member
 
Location: Utah

Join Date: Aug 2013
Posts: 4
Default

Here is what appears:
[email protected]:~$ echo $PATH
/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
[email protected]:~$
brymerr921 is offline   Reply With Quote
Old 08-12-2013, 07:08 PM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
Default

That again looks right. Not sure what to ask you to try next. In case no one from the west coast helps further tonight we can look at this tomorrow.
GenoMax is offline   Reply With Quote
Old 08-13-2013, 01:22 AM   #7
emq
Junior Member
 
Location: NW, Germany

Join Date: Jul 2012
Posts: 2
Default

Hi brymerr,

I am actually not sure but I think you have not to use
HTML Code:
 sudo ./setup.sh
. Try it without sudo, as my experience was that I could install 2.7 only locally and for this you don't need sudo.

The link you created for bash did not work for root -- maybe.
emq is offline   Reply With Quote
Old 08-13-2013, 04:09 AM   #8
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default

http://seqanswers.com/forums/showthread.php?t=30045
JackieBadger is offline   Reply With Quote
Old 09-18-2013, 06:30 AM   #9
justindyson
Junior Member
 
Location: Cambridge, UK

Join Date: Sep 2013
Posts: 1
Default

I had the same issue. It's just because /bin/sh is not in the rpm database. To get round this I installed the STLinux "provides" RPM. This populates the database without installing anything and this happens to include /bin/sh:

Information: http://stlinux.com/install/ubuntu
Pick the latest version from here: http://download.stlinux.com/pub/stlinux/2.4/misc/

Simply do a:

Code:
rpm -ivh --force-debian stlinux24<version>.rpm
and then

Code:
sudo apt-get install ia32-libs
sudo ln -s /bin/true /bin/rocks
sudo ln -s /usr/bin/lspci /sbin/lspci
sudo dpkg-reconfigure dash   (select no)
sudo ./setup.sh
It should install without any problems.
justindyson is offline   Reply With Quote
Old 10-11-2014, 08:42 AM   #10
yifangt
Member
 
Location: Canada

Join Date: Feb 2011
Posts: 61
Default Which one is the latest STLinux

I saw this list, but which one should I pick?
Code:
stlinux24-host-STLinux_deps-20100401-1.i386.rpm 01-Apr-2010 17:01  4.2K  
[   ] stlinux24-host-STLinux_deps-20100427-1.i386.rpm 28-Jun-2010 14:56  4.4K  
[   ] stlinux24-host-STLinux_deps-20110126-1.i386.rpm 26-Jan-2011 11:47  4.4K  
[   ] stlinux24-host-STLinux_deps-20110331-1.i386.rpm 31-Mar-2011 12:30  4.5K  
[   ] stlinux24-host-STLinux_deps-20110614-1.i386.rpm 14-Jun-2011 10:40  4.5K  
[   ] stlinux24-host-STLinux_deps-20111020-1.i386.rpm 20-Oct-2011 11:07  5.7K  
[   ] stlinux24-host-STLinux_deps-20120508-1.i386.rpm 08-May-2012 14:20  5.7K  
[   ] stlinux24-host-STLinux_deps-20120731-1.i386.rpm 01-Aug-2012 11:23  6.1K  
[   ] stlinux24-host-STLinux_deps-20121030-1.i386.rpm 30-Oct-2012 14:41  7.1K  
[   ] stlinux24-host-STLinux_deps-20130321-1.i386.rpm 21-Mar-2013 14:11  7.1K  
[   ] stlinux24-host-STLinux_deps-20131122-1.i386.rpm 22-Nov-2013 13:43  7.1K  
[   ] stlinux24-host-STLinux_deps-20140120-1.i386.rpm 23-Jan-2014 16:04  7.2K
I assumed the last one,
Code:
stlinux24-host-STLinux_deps-20140120-1.i386.rpm
and installed it. The problem is still there. Any idea? Thanks!
yifangt is offline   Reply With Quote
Old 06-04-2015, 09:00 AM   #11
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 123
Default

hello,
I have a local installation of newbler but here the error message:

Code:
Warning: One or more of the following libraries was not found

   zlib.i386, libXi.i386, libXtst.i386, libXaw.i386

Without these libraries, 454 Life Sciences software may not run correctly.  Consult the product documentation for more information.

could you help me?
thankyou
mido1951 is offline   Reply With Quote
Old 06-04-2015, 11:52 AM   #12
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
Default

What flavor of unix/linux are you running?

Here is a relevant thread that will help: http://ubuntuforums.org/showthread.php?t=1624351 See post #3.
GenoMax is offline   Reply With Quote
Old 06-05-2015, 01:45 AM   #13
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 123
Default

i have Ubuntu 12.04LTS.
I installed the librairies ia32-libs.
but it's the same problème.
Thankyou
mido1951 is offline   Reply With Quote
Old 06-05-2015, 01:53 AM   #14
dschika
Member
 
Location: Zurich

Join Date: Mar 2010
Posts: 56
Default

Maybe this thread helps?
http://seqanswers.com/forums/showthread.php?t=25339
dschika is offline   Reply With Quote
Reply

Tags
error, install, newbler, ubuntu

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 10:27 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO