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Old 05-25-2011, 03:33 PM   #1
gene_x
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Default 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!
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Old 05-25-2011, 08:23 PM   #2
dp05yk
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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).
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Old 05-25-2011, 08:46 PM   #3
gene_x
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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?
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Old 05-25-2011, 08:54 PM   #4
dp05yk
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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!
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Old 05-25-2011, 08:57 PM   #5
gene_x
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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..
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Old 05-25-2011, 09:27 PM   #6
gene_x
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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??
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Old 05-26-2011, 06:02 AM   #7
dp05yk
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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.
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Old 05-26-2011, 06:57 AM   #8
gene_x
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I tried to download an linux version and it indeed solved the problem!
But the unzip commend still doesn't work...

Thanks a lot!
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Old 05-26-2011, 08:49 AM   #9
gene_x
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Quote:
Originally Posted by dp05yk View Post
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!
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Old 10-27-2013, 04:15 AM   #10
maize
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Smile bowtie installation

Quote:
Originally Posted by gene_x View Post
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!
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Old 10-27-2013, 08:41 AM   #11
gene_x
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Quote:
Originally Posted by maize View Post
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.
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Old 11-01-2013, 08:25 AM   #12
geneW
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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!
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Old 11-01-2013, 08:47 AM   #13
dpryan
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Ther's nothing to make when you download the precompiled version. Just move the executables somewhere convenient.
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Old 11-01-2013, 08:47 AM   #14
GenoMax
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Quote:
Originally Posted by geneW View Post
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.
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Old 11-01-2013, 08:53 PM   #15
geneW
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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
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Old 11-02-2013, 02:39 AM   #16
dpryan
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Everything starting with bowtie2 is an executable there. Just move them all into your path.
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Old 12-17-2013, 11:22 AM   #17
patrickwang
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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.
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Old 12-17-2013, 12:24 PM   #18
dpryan
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Quote:
Originally Posted by patrickwang View Post
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="$PATH:~/bin"
The you can just type "bowtie2" or whatever and things will work with less typing.
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Old 08-04-2014, 07:33 AM   #19
simobioinfo
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Hello! I'm a newbie trying to install bowtie.
I unzipped the source file and then I compiled it
After I tried to add it to my path, I see this message in my shell
"Il comando non può essere localizzato perché "/usr/bin" non è incluso nella variabile d'ambiente PATH".
No command function anymore... what can I do to solve this problem?
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Old 08-04-2014, 07:50 AM   #20
dpryan
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So include /usr/bin in the PATH:
Code:
export PATH="$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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