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-   -   How to install Bowtie (http://seqanswers.com/forums/showthread.php?t=11617)

gene_x 05-25-2011 02:33 PM

How to install Bowtie
 
Hi, all,
I'm new to informatics and I'm trying to install Bowtie in our cluster. I've downloaded the zip file and don't know how to proceed from there. Can anyone help me on that? I'm using a Mac.
Thanks a lot!

dp05yk 05-25-2011 07:23 PM

Unzip it, navigate to the folder using your Terminal program (if you can't find terminal, press command + spacebar to bring up spotlight and type "Terminal").

If you've never used a bash terminal before, make sure you unzip your folder somewhere easy to find, like your desktop. Then from terminal type "cd desktop", and then "ls", to view all files on your desktop. Then "cd folder_name" where folder_name = bowtie folder.

Once inside this folder, just type "make". It should compile as long as you have Developer Tools installed on your mac (or the applicable compiler).

gene_x 05-25-2011 07:46 PM

thanks for your reply! I actually know how to navigate the terminal.. I downloaded the zip file onto our server and tried to unzip the file by commend: unzip bowtie-0.12.7-macos-10.5-x86_64.zip

Then this message pops up:

Archive: bowtie-0.12.7-macos-10.5-x86_64.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of bowtie-0.12.7-macos-10.5-x86_64.zip or
bowtie-0.12.7-macos-10.5-x86_64.zip.zip, and cannot find bowtie-0.12.7-macos-10.5-x86_64.zip.ZIP, period.

What should I do with this?

dp05yk 05-25-2011 07:54 PM

Strange... how do you enter the filename... do you hit "tab" after typing, say, "bowtie" and let the terminal autocomplete the filename?

Try renaming the zip file to something really simple like "bowtie.zip" and try again.

What you can always do is just unzip the file on your mac via. the GUI and then upload the unzipped folder to your server!

gene_x 05-25-2011 07:57 PM

I did hit "tab" and the filename is what appears on the bowtie website. I tried to use simple names as "bowtie.zip" but it had the same problem...
I know just unzip the file on my computer and then upload them.. this is not the best way to do it apparently..

gene_x 05-25-2011 08:27 PM

OK. I've done that and tried the Bowtie tutorial and got an error message:
-bash: ./bowtie: cannot execute binary file

I think the reason is when I tried the commend "make" in the bowtie directory, an error messages pops up:
make: *** No targets specified and no makefile found. Stop.
when I tried "make all", another error message:
make: *** No rule to make target `all'. Stop.
or "make clean"
make: *** No rule to make target `clean'. Stop.

What's the problem here??

dp05yk 05-26-2011 05:02 AM

Ok. Looks like Bowtie comes precompiled so there's no makefile. The problem for you is that ./bowtie doesn't work.

Even though you're using a mac, you _do not_ want to download the mac version of bowtie since you're putting it on your cluster. Your cluster is likely linux-based so you'll want to get the linux version of Bowtie. I'm assuming this is what is causing the unzip error as well.

gene_x 05-26-2011 05:57 AM

I tried to download an linux version and it indeed solved the problem!
But the unzip commend still doesn't work...

Thanks a lot!

gene_x 05-26-2011 07:49 AM

Quote:

Originally Posted by dp05yk (Post 42554)
Ok. Looks like Bowtie comes precompiled so there's no makefile. The problem for you is that ./bowtie doesn't work.

Even though you're using a mac, you _do not_ want to download the mac version of bowtie since you're putting it on your cluster. Your cluster is likely linux-based so you'll want to get the linux version of Bowtie. I'm assuming this is what is causing the unzip error as well.

I solved the problem.. so the reason I couldn't unzip the zip file is that it's incomplete.. I tried to re-download the file and now the unzip commend works!

maize 10-27-2013 03:15 AM

bowtie installation
 
Quote:

Originally Posted by gene_x (Post 42573)
I solved the problem.. so the reason I couldn't unzip the zip file is that it's incomplete.. I tried to re-download the file and now the unzip commend works!

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!

gene_x 10-27-2013 07:41 AM

Quote:

Originally Posted by maize (Post 120079)
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.

geneW 11-01-2013 07:25 AM

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!

dpryan 11-01-2013 07:47 AM

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

GenoMax 11-01-2013 07:47 AM

Quote:

Originally Posted by geneW (Post 120590)
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.

geneW 11-01-2013 07:53 PM

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

dpryan 11-02-2013 01:39 AM

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

patrickwang 12-17-2013 10:22 AM

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 12-17-2013 11:24 AM

Quote:

Originally Posted by patrickwang (Post 127742)
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:

Code:

export PATH="$PATH:~/bin"
The you can just type "bowtie2" or whatever and things will work with less typing.

simobioinfo 08-04-2014 06:33 AM

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 08-04-2014 06:50 AM

So include /usr/bin in the PATH:
Code:

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.


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