Installing 454 Data Analysis v2.6 on Ubuntu 10.04 LTS

This is a backup text about the problems I had when installing that software, the solution I finally achieved and the opened questions remaining.

- First of all, I tried to execute like this

./setup.sh

with the following result:

export: 9: software/DataAnalysis_2.6_All/setup.sh: bad variable name

- Then, I tried to execute from a copy I burned into a CD. The result was:

i) on the awful white backgrounded installing window:

/sbin/lspci: not found

ii) window with the text

Cannot execute command: type rocks2>&1

- On SeqAnwers it was the solution for me. But as well some strange advices.
First, some people was telling to try:

sudo ln -s /bin/true ~/bin/rocks
sudo ./setup.sh

Since /bin/true returns true, we are cheating the install program. I didn't want to do that and moreover some people was being able to install but getting some errors afterwards.

- Son on SeqAnwers.com I found a solution, altough really long. I actually would like to resolve the errors I am describing above, to get a fast forward install process but... meanwhile:


I am trying the first one.
pico .bashrc

On the pico editor, at the end of the file, type:

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

Then, create directories:

cd /opt
sudo mkdir 454
sudo mkdir 454/apps
sudo mkdir 454/apps/jre

cd user_directory_at_home/454soft/DataAnalysis_All/packages
cp newbler_CLI-2.6.i686.tgz /opt/454

(Here I had another problem. I first did copy the 64 bits package and I found I could not execute sfffile and similar SFFtools, stil wondering why...)

cp assembly_GUI_2.6.noarch.tgz /opt/454/apps
cp (the same with mapper)
cp (the same with amplicon)

cd opt/454
sudo tar -xzvf newbler...tgz
cd apps
sudo tar -xzvf assembly...tgz
sudo (the same with mapper)
sudo (the same with amplicon)

sudo rm -r .*tgz
cd ..
sudo rm -r .*tgz

ls /opt/454

apps bin config

ls /opt/454/apps

amplicons assembly jre mapper

Now that everything is ready, we have to create the symbolic linnks:
(if you create a link by error, you can erase it with # sudo unlink name_of_link)

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

cd ..
cd assembly/jre
sudo ln -s ../../jre/jre1.6.0_13 jre1.6.0_13
cd ../amplicon/jre
sudo ln (exactly the same)
cd ../mapper/jre
sudo ln (exactly the same)

finally:

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


TEST! Thank you to WaltL from SeqAnswers.com forum: http://seqanswers.com/forums/showthread.php?t=8944

Finally, I hope to find the anwers to the initial problems, to can get an easier installation.

best wishes!