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Old 01-18-2011, 11:00 AM   #1
WaltL
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Default Installing Newbler 2.5.3 on 64 bit Ubuntu...anyone???

Just wondering if anyone has managed a successful install of Newbler 2.5.3 on later versions of Ubuntu.

I have the previous version installed and working fine on Ubuntu 10.04. However, the latest version of Newbler uses a third party installer (Nixstaller ver. 0.5.1) which crashes very early on with the following error:
Cannot execute command: type rocks2>&1
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Old 01-18-2011, 09:54 PM   #2
ulz_peter
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I got the very same problem. I didn't resolve it (my knowledge of shell scripting is limited...). I resolved another error where Nixstaller tried to find lspci under /sbin which is under /usr/bin in Ubuntu but the type rocks problem didn't change...

Maybe I'll switch to a ReHat derived distribution as the Roche engineers seem to only bear that in mind.
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Old 01-19-2011, 12:23 AM   #3
sklages
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... might be overkill .. but the result is what count :-)
- install a redhat in a virtual machine
- install roche newbler on the redhat system
- copy the roche directory tree on your "working" system

Usually Roche's installer is a catastrophe; changing though from version to version .. :-)

my 2p,
Sven
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Old 01-19-2011, 04:25 AM   #4
WaltL
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I worked on it most of the day and finally got it installed.

It is not too difficult, but you cannot use the installer. I am performing a test assembly this morning and I will post installation instructions a bit later today.

Walt
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Old 01-20-2011, 12:56 PM   #5
WaltL
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Installation of Newbler version 2.5.3 on Ubuntu 10.04.1 (Lucid Lynx) without using the supplied Nixstaller.

Important Note: Do not cut and paste the commands below. Type them in.

Important Note 2: This installation should also work with earlier versions of Ubuntu. Later versions of Ubuntu, 10.04.1 and 10.10 (Maverick Meerkat), did not come with Sun java as did previous versions. I have also tested this installation using java-6-openjdk that comes with 10.04 and 10.10 and it works just fine.

I'm sure there are probably easier/faster ways to accomplish this install, however, this is a tested work around and I have tried and tested. I wrote this with detailed instructions so that those with little or limited unix/linux experience should be able install Newbler without too much difficulty.

My apologies to those who find the step by step approach to be over-kill.


1) Everything needs to be done with root privileges so it's easier to just become root (if you can't this, better stop now and get someone to help you with the install).

2) If you have Newbler already installed, rename the directory opt/454 to something like opt/454_older.ver.number and go to step 3.

If Newbler has never been installed, you will also need to add opt/454/bin to your path. Different ways to do this. I did it by creating an .sh file that contains the path and placing the file in /etc/profile_d
Example:
/etc/profile_d~# pico -w 454.sh

Once in the pico editor type the following:

export PATH=$PATH:/opt/454/bin

exit editor with CtrlX and yes to save. You will need to log off and then log back on for the path change to take place.
Now open a bash shell and enter echo $PATH at the prompt to verify that the path has been added and become root again.

3) Navigate to the indicated directories below and create the following directories in the indicated locations:

opt/~# mkdir 454
opt/454~# mkdir apps
opt/454/apps~# mkdir jre

4) Copy the Newbler tarball file DataAnalysis.tgz to directory /opt/454 and extract (either at command line using tar -xzvf DataAnalysis.tgz or with the Ubuntu GUI package manager)

5) Remove the file DataAnalysis.tgz after you have extracted it.

6) Navigate to the directory DataAnalysis_2.5.3/packages/ and copy the following .tgz files to the indicated destinations:

/opt/454/DataAnalysis_2.5.3/packages~# cp newbler_CLI-2.5.3.x86_64.tgz ../../
/opt/454/DataAnalysis_2.5.3/packages~# cp assembly_GUI_2.5.3.noarch.tgz ../../apps
/opt/454/DataAnalysis_2.5.3/packages~# cp mapper_GUI_2.5.3.noarch.tgz ../../apps
/opt/454/DataAnalysis_2.5.3/packages~# cp amplicon_GUI_2.5.3.noarch.tgz ../../apps

7) Navigate to the directories shown below and extract the the four tarballs. You should remove each .tgz file after extracting it.

opt/454~# tar -xzvf newbler_CLI-2.5.3.x86_64.tgz
opt/454/apps~# tar -xzvf assembly_GUI_2.5.3.noarch.tgz
opt/454/apps~# tar -xzvf mapper_GUI_2.5.3.noarch.tgz
opt/454/apps~# tar -xzvf ampicon_GUI_2.5.3.noarch.tgz

8) Now remove the directory DataAnalysis_2.5.3 located in opt/454

If you've done everything correctly to this point, your directory structure will look like this:

/opt/454~# ls
apps bin config

/opt/454/apps~# ls
amplicons assembly jre mapper


Now we need to make multiple symbolic links to get everything to run. You can do this two ways:

A) Use the command gksudo nautilus which opens a GUI with root privileges and then create the the required symbolic links graphically by copying and pasting the target link to its appropriate destination directory.
B) Make the symbolic links at command line (as I have shown).


First make the primary java link:

9) Navigate to the directory /opt/454/apps/jre and create a symbolic link to the java that Ubuntu is using and give it the name of the java directory that Newbler wants to use: jre1.6.0_13
Use either A or B, not both!

A) For early Ubuntu versions with Sun Java

/opt/454/apps/jre~# ln -s /usr/lib/jvm/java-6-sun jre1.6.0_13

B) For later Ubuntu versions without Sun Java installed:

/opt/454/apps/jre~# ln -s /usr/lib/jvm/java-6-openjdk jre1.6.0_13

You can check that the link was made by doing an ls command and you should see one of the following:
jre1.6.0_13 -> usr/lib/jvm/java-6-sun/ OR jre1.6.0_13 -> usr/lib/jvm/java-6-openjdk/


Now, you need to make symbolic links for the three applications (amplicon, assembly, and mapper) back to the link that you just created in /opt/454/apps/jre
(again, you can also do this in Nautilus by just copying the link you created in opt/454/apps/jre and then pasting into the appropriate directories below)

10) Navigate to the directories shown below and create the symbolic link in each as follows:

/opt/454/apps/assembly/jre~# ln -s ../../jre/jre1.6.0_13 jre1.6.0_13
/opt/454/apps/amplicon/jre~# ln -s ../../jre/jre1.6.0_13 jre1.6.0_13
/opt/454/apps/mapper/jre~# ln -s ../../jre/jre1.6.0_13 jre1.6.0_13

Again, an ls command from within each jre directory should show the following:
jre1.6.0_13 -> ../../jre/jre1.6.0_13

Now you need to create the final four symbolic links, these are all from within the /opt/454/bin directory, to the their respective application executables which listed below:
1) /opt/454/apps/assembly/bin/gsAssembler
2) /opt/454/apps/mapper/bin/gsMapper
3) /opt/454/apps/amplicon/bin/gsAmplicon
4) /opt/454/apps/amplicon/bin/doAmplicon


11) Navigate to opt/454/bin and create the following symbolic links:

/opt/454/bin~# ln -s ../apps/assembly/bin/gsAssembler gsAssembler
/opt/454/bin~# ln -s ../apps/mapper/bin/gsMapper gsMapper
/opt/454/bin~# ln -s ../apps/amplicons/bin/gsAmplicon gsAmplicon
/opt/454/bin~# ln -s ../apps/amplicons/bin/doAmplicon doAmplicon


12) Test each program at command line by typing the program name, e.g. gsAssemble, gsMapper, or gsAmplicon.

In each case the GUI should launch. If it doesn't, it is likely due to an error in creation of the symbolic links for either java or the executables.
Note: that doAmplicon is a command line program and does not launch a GUI but goes to a > prompt.

Happy Assembling!
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Old 01-24-2011, 02:15 AM   #6
just_testing
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Thank you for manual installation instructions. I tried to follow them but still can't get gsAmplicon to work properly, the GUI does launch but then it won't create a new project and trying to open an old project results to an empty error dialog. Has anyone else tried to use gsAmplicon with this installation?
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Old 01-24-2011, 03:21 AM   #7
jvhaarst
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The Data Processing rpm's can be 'installed' like this:

First download the DataProcessing_2.5.3.tgz file.
Extract that file in a place of your liking.

In a terminal, go to the directory packages of the extracted file, and do this :

for file in gsReporter-2.5.3-1.x86_64.rpm gsRunBrowser-2.5.3-1.i686.rpm gsRunProcessor-2.5.3-1.x86_64.rpm gsSupportTool-1.23-1.i386.rpm;do rpm2cpio $file | cpio -idmv ; done

This will extract the contents of all the RPMs in the local directory, in a /opt subdirectory.
Now simply move the different applications to the place where you want them, like this :

mv -v ~/bin/454_2.5.3/DataProcessing_2.5.3_All/packages/opt/454/apps/* ~/bin/454_2.5.3/apps/

Then create links for the applications on a spot in your path :

cd ~/bin/454_2.5.3/bin ; ln -vs ../apps/gs*/bin/* .
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Old 01-26-2011, 06:09 AM   #8
Abbe
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Smile Installing Newbler 2.5.3 on 64 bit Ubuntu

We just did it!

It took us 45 min.Thanks for the installation instruction.
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Old 02-02-2011, 10:54 AM   #9
rad
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Assuming you have a bin directory in your $HOME, and its in your $PATH

ln -s /bin/true ~/bin/rocks

then run the installer.
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Old 02-02-2011, 11:10 AM   #10
sklages
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In every installer of every version of the roche suite, they always introduce something weird, to remove it in the next version of the installer .. take a bet that in the next major release of the suite 'rocks' has been eliminated (but something new has been introduced) ..

SCNR,
Sven
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Old 02-08-2011, 05:04 AM   #11
jvhaarst
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I have done a quick analysis of the basecalling differences between 2.3 and 2.5.3:


The higher resolution pdf (with summary information on the reads) is available at http://db.tt/gbL9pYi
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Old 03-08-2011, 07:14 AM   #12
Dane
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I have installed the new software successfully but am now not able to use the sfffile command in the terminal, anyone else having this problem and know an easy fix?
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Old 03-08-2011, 08:03 AM   #13
sklages
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Quote:
Originally Posted by Dane View Post
I have installed the new software successfully but am now not able to use the sfffile command in the terminal, anyone else having this problem and know an easy fix?
What did you install (what is the "new software")? sfffile is part of the DataAnalysis package.

What does it mean that you are "not able to use the sfffile command in the
terminal"?

You should probably set your (command) PATH (use your installation path):

export PATH="/path/to/roche/datanalysis/bin:$PATH"

and then type 'sfffile'.

To make this permanent use e.g. .bashrc

Sven
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Old 03-08-2011, 08:10 AM   #14
Dane
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Quote:
Originally Posted by sklages View Post
What did you install (what is the "new software")? sfffile is part of the DataAnalysis package.
Sven
The data analysis pkg

Quote:
Originally Posted by sklages View Post
What does it mean that you are "not able to use the sfffile command in the
terminal"?
Sven
When i use the "sfffile -i mapped.txt -o mapped.sff ../sff/*" command it returns that the "command doesnt exist"

Quote:
Originally Posted by sklages View Post
You should probably set your (command) PATH (use your installation path):

export PATH="/path/to/roche/datanalysis/bin:$PATH"

and then type 'sfffile'.

To make this permanent use e.g. .bashrc

Sven
I don't understand how to recode the path for the sfffile. It looks like its trying to use an old folder for the sfffile command.

This is what the terminal is spitting out:
bash: /path/to/roche/datanalysis/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/454/bin: No such file or directory


If you could give me specifics that would be appreciated since I still dont understand Ubuntu all that great yet.

Last edited by Dane; 03-08-2011 at 08:15 AM.
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Old 03-08-2011, 08:32 AM   #15
sklages
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Quote:
Originally Posted by Dane View Post
The data analysis pkg

When i use the "sfffile -i mapped.txt -o mapped.sff ../sff/*" command it returns that the "command doesnt exist"



I don't understand how to recode the path for the sfffile. It looks like its trying to use an old folder for the sfffile command.

This is what the terminal is spitting out:
bash: /path/to/roche/datanalysis/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/454/bin: No such file or directory


If you could give me specifics that would be appreciated since I still dont understand Ubuntu all that great yet.
Here may be the problem, you should replace the path "/path/to/roche/datanalysis/bin" with the real bin path,
I suspect this is "/opt/454/bin".
So you need to export this path,

export PATH="/opt/454/bin:$PATH"

on the other hand, /opt/454/bin has already been there.
Have you installed the software to /opt/454?

Have a look at /opt/454/bin and see what's inside,

ls /opt/454/bin/

Do you see all programs?

Is this a 64bit or 32bit Ubuntu? Did you install the correct i686 or x86_64 package?

cheers,
Sven
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Old 03-08-2011, 08:48 AM   #16
Dane
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I installed a new directory for a "local" install rather than system. So the new directory is home/dane/454/

The old directory is still in opt/454/bin with all the files.

64bit Ubuntu, Im not sure which package the installer used. However, I tried replacing any of the i686 tarballs that might have been installed instead of the x86 and then the programs wouldn't assemble and would come up with syntax errors.
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Old 03-08-2011, 08:53 AM   #17
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No, do not mix files. If you see all the file in /opt/454/bin what gives you a

file /opt/454/bin/sfffile

What gives you

/opt/454/bin/sfffile

Sven
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Old 03-08-2011, 10:29 AM   #18
Dane
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Quote:
Originally Posted by sklages View Post
No, do not mix files. If you see all the file in /opt/454/bin what gives you a

file /opt/454/bin/sfffile

What gives you

/opt/454/bin/sfffile

Sven
/opt/454/bin/sfffile gives me permission denied so I have to run it with sudo.

I went ahead and tried /454 which is where my new install is located and its telling me that the directory doesn't exist.
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Old 03-08-2011, 10:42 AM   #19
sklages
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Quote:
Originally Posted by Dane View Post
/opt/454/bin/sfffile gives me permission denied so I have to run it with sudo.

I went ahead and tried /454 which is where my new install is located and its telling me that the directory doesn't exist.
When you have installed your package in /opt/454 with 'sudo' then you have to change
the permissions (as well with 'sudo') accordingly, so that you can access the files/progs.

About your "new" install you wrote you have installed it in "/home/dane/454/"; where
comes the "/454" from?

If your installation is in "/home/dane/454/" (hopefully without 'sudo'), you should alter
your PATH accordingly,

export PATH="/home/dane/454/bin:$PATH"

Sven
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Old 03-08-2011, 10:53 AM   #20
Dane
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Quote:
Originally Posted by sklages View Post

If your installation is in "/home/dane/454/" (hopefully without 'sudo'), you should alter
your PATH accordingly,

export PATH="/home/dane/454/bin:$PATH"

Sven
Awesome, that fixed the pathing, thank you very much for you help. Kudos
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