[dpryan]

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

[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]

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.

[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]

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]

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]

You just need to edit ~/.bashrc

[simobioinfo]

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

[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]

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 ?

[dpryan]

You just need to do what Genomax and I mentioned.

BTW, you would do well to buy a book on using Linux (or Unix or even Mac OS X from the command line). This sort of thing should be covered in such a book.

[simobioinfo]

Thank you again for your help. I solved my problems with shell and also to add bowtie to PATH.
Bye
Simona

[zillur]

Bow-tie

Hey Guys,
I am new here. I have a problem to run bow tie on my mac. Here is my command line on terminal: Mds-MacBook-Pro:bioinformatics ZILLURRAHMAN$ cd bow-tie
Mds-MacBook-Pro:bow-tie ZILLURRAHMAN$ ls
2012_Lab_Exercise_2.doc
CGRL - Installing and Using Bowtie.webarchive
How to install Bowtie - SEQanswers.webarchive
Installation and use of Bowtie | Bioinformatics at Viikki campus.webarchive
Trinity (runs local) | Applied Bioinformatics Journal Club.webarchive
bowtie2-2.2.3
ernestturro_mappingpractical.pdf
Mds-MacBook-Pro:bow-tie ZILLURRAHMAN$ cd bowtie2-2.2.3
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ make

Then it showed an error message like this:

Agreeing to the Xcode/iOS license requires admin privileges, please re-run as root via sudo.

What should I do now?

[GenoMax]

I assume you have the latest Xcode installed. Try running the make as follows.

$ sudo make

As an aside, please avoid using spaces in names with OS X. Replace the spaces with an "_" when you need a delimiter.

[zillur]

Thank you very much. With this command the terminal showing this message:
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ sudo make
make: *** No targets specified and no makefile found. Stop.

what should I do now?