[simobioinfo]

Thank you so much... my shell now is functional.
Now I have to add bowtie2 to path, which was the cause for the previous problem.
I downloaded -source.zip, unzipped it and then compiled.
However, if I digit "bowtie2", I have this message "command not found".
What's the problem? what I have to do to add bowtie2 to PATH without damage in my system ?

[GenoMax]

If you are logged into your user account then you should be able to edit your .bashrc file by using an appropriate text editor such as pico/nano by doing

$ pico ~/.bashrc

After you add the export line the .bashrc remember to save the file and then source it.

$ source ~/.bashrc

or you could log out and then log back in again (when the .bashrc would be re-read). Using "source" command allows you to read the profile without having to log out then in.

[simobioinfo]

Do I have to do these changes as root? If I digit ~/.bashrc, I heve the following message: permission denied

[dpryan]

You just need to edit ~/.bashrc

[simobioinfo]

Thank you and excuse me but I registered to the site just few minutes ago. The command function even if I have also to digit
export PATH="$PATH:/bin"
I have another question: How do I make permanent this command? When I close terminal, the problem returns.

[dpryan]

So include /usr/bin in the PATH:

export PATH="$PATH:/usr/bin"

For future reference, it's usually easier for people to diagnose problems if (1) the error messages are translated into English and (2) you show exactly what you did that produced them.

[simobioinfo]

Hello! I'm a newbie trying to install bowtie.
I unzipped the source file and then I compiled it
After I tried to add it to my path, I see this message in my shell
"Il comando non può essere localizzato perché "/usr/bin" non è incluso nella variabile d'ambiente PATH".
No command function anymore... what can I do to solve this problem?

[dpryan]

But what should I do to move them into the path.

I also installed the Bowtie2 on a linux system. After unzip, the bowtie2 folder contains AUTHORS bowtie2-align-debug bowtie2-inspect example MANUAL.markdown TUTORIAL
bowtie2 bowtie2-build bowtie2-inspect-debug LICENSE NEWS VERSION
bowtie2-align bowtie2-build-debug doc MANUAL scripts

and three subfolers doc, example, and scripts.

On every system, I create a "~/bin" folder to just move personal executables like that into. Then I just edit "~/.bashrc" and add the following at the end:

export PATH="$PATH:~/bin"

The you can just type "bowtie2" or whatever and things will work with less typing.

[patrickwang]

But what should I do to move them into the path.

I also installed the Bowtie2 on a linux system. After unzip, the bowtie2 folder contains AUTHORS bowtie2-align-debug bowtie2-inspect example MANUAL.markdown TUTORIAL
bowtie2 bowtie2-build bowtie2-inspect-debug LICENSE NEWS VERSION
bowtie2-align bowtie2-build-debug doc MANUAL scripts

and three subfolers doc, example, and scripts.

[dpryan]

Everything starting with bowtie2 is an executable there. Just move them all into your path.

[geneW]

I'm installing it in Linux on cluster. Below are the files in the unziped folder, which is under desktop folder. Which are the executables to be used?



AUTHORS bowtie2-align-debug bowtie2-inspect example MANUAL.markdown TUTORIAL
bowtie2 bowtie2-build bowtie2-inspect-debug LICENSE NEWS VERSION
bowtie2-align bowtie2-build-debug doc MANUAL scripts

[GenoMax]

I'm also trying to install bowtie. What I did:

download bowtie2-2.1.0-linux-x86_64.zip
unzip successfully

the above just talked to "make". It did not work for me as no make file in the unzip folder.

I need instructions on what's next after unzip.

Thanks!

What OS are you using?

Edit: As Devon pointed out above there is nothing to "make" when you download a pre-compiled ready to use copy.

[dpryan]

Ther's nothing to make when you download the precompiled version. Just move the executables somewhere convenient.

[geneW]

I'm also trying to install bowtie. What I did:

download bowtie2-2.1.0-linux-x86_64.zip
unzip successfully

the above just talked to "make". It did not work for me as no make file in the unzip folder.

I need instructions on what's next after unzip.

Thanks!

[gene_x]

Hi buddy,

I noticed that you installed the bowtie successfully. Now i also downloaded the bowtie_zip file and unzip it. but i cannot install it smoothly. Could you share your experience with me ? thanks in advance!

My problem was that the files were incomplete.. Once I got the right file, unzip it and then follow the instructions mentioned above was fine.