[horvathdp]

Cool. it now no longer hangs up on samtools! You rock. However, now it can't find bowtie :-)

One step closer though :-)

Error, path to required bowtie2 cannot be found at ./alignReads.pl line 245.

I don't suppose there is an ubuntu script for that is there?

[GenoMax]

Getting samtools via "apt get" puts it in the "correct" spot in system directories (/usr/bin perhaps). So now if you do

$ which samtools

You should see the full path to the executable.

[GenoMax]

Cool. it now no longer hangs up on samtools! You rock. However, now it can't find bowtie :-)

One step closer though :-)

Error, path to required bowtie2 cannot be found at ./alignReads.pl line 245.

I don't suppose there is an ubuntu script for that is there?

You can also "apt get" bowtie2.

[horvathdp]

Awesome! however, tried and got:
E: Unable to locate package bowtie2

[horvathdp]

I ran the sudo apt-get update #recommended from another website, but still no joy.

[GenoMax]

Which Ubuntu are you running (13.10)?

[horvathdp]

Looks like my instance is running:
Ubuntu 12.04 Xfce GUI v2

[horvathdp]

Ahhh...too old a version to have bowtie2 . I was able to get bowtie to load, and now my program seems to be running. This apt get command is way cool.

In case anyone else runs into this problem. I found the directory of available programs at: https://apps.ubuntu.com/cat/search/?q=rsem&op=

Mr. GenoMax, you win the prize. I am in your debt! Don't know if you go to meetings like PAG, but if so, look me up and I'll buy you a beer :-)

[GenoMax]

Get the pre-compiled version of bowtie2 then: http://sourceforge.net/projects/bowt...4.zip/download

You are going to have the same issues with $PATH as before so it may be time to look at that UNIX website from the Korf lab.

[horvathdp]

Reading on. I suspect when i can figure out where the SAMtools and bowtie programs I just installed are located, I'll be able to put bowtie2 in the correct place :-)

[GenoMax]

Reading on. I suspect when i can figure out where the SAMtools and bowtie programs I just installed are located, I'll be able to put bowtie2 in the correct place :-)

That is one way to do things. The easier option would be to just modify your $PATH. That way you could keep multiple versions of programs around (in different directories) and just use the right $PATH as needed.

[horvathdp]

OK, so I cheated a bit (a person with a bit more computer savvy than yself walked into my office while I was working on this). So, the first thing i did was look for the samtools and bowtie programs uploaded by the apt-get command. These were both in the usr/bin folder. Thus, I moved the bowtie2-2.1.0 folder there. I tried which bowtie2 and got nothing (which was when my visitor arrived) She then showed me how to find hidden files (ls -a) and a google search indicated a couple of different options. Her first instinct was to change the bashrc file, so we used the cmd "emacs .bashrc" to open this file so we could alter it and added the following to the end of that file export PATH=/usr/bin/bowtie2-2.1.0/:$PATH - note we added the slash after the folder name because we thought it might be needed because bowtie2 came in a folder with executables inside. After saving (ctr X,ctr S) and then exiting (ctr X ctr C) and then gave the command $ source .bashrc to engage the change. A test using which bowtie2 failed again. Thus more reading indicated we should (also?) modify the .profile file. Thus, we emacs into the .profile file and added PATH="$PATH:/usr/bin/bowtie2-2.1.0" to the end of that file and engaged it with the command $ source .profile . That seemed to do the trick: which bowtie2 gives: /usr/bin/bowtie2-2.1.0//bowtie2. We are not sure about the extra slashes, but she doesn't think it will matter. Sound right? Any idea if we actually needed to modify the .bashrc file?

[GenoMax]

Modifying the .bashrc meant that the changes will be applied everytime you log in. You won't need to amend the $PATH each time.

The extra slash should be ok but if you want to be precise take it out of the bashrc PATH statement.

BTW: That was not cheating. You always learn faster from someone next to you, who can see what is on your screen.

[westerman]

Thanks GenoMax, will do here momentarily:
@Rick, sorry to frustrate. I did type "which samtools" but nothing happened- even when I cd'd into the samtools directory. see below:

No results from 'which' means that you do not have samtools installed in your path. No results from simply typing in 'samtools' means the same thing.

I am glad to see that you got samtools installed. And perhaps more importantly help from a knowledgeable person. I agree with GenoMax: it was not cheating. Getting local help on basic Unix from someone who can see your screen -- and who can interact in real time -- is better that relying on us in SeqAnswers. Make sure you treat your local help nicely. Chocolate is usually appropriate -- personally I like chocolate covered donuts.