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Old 12-05-2011, 03:00 AM   #1
MMPE
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Default Installation of Burrows-Wheeler Alignment Tool (bwa) on Mac

Hi I am new to the bioinformatic field. I just want to know how I could install the bwa in my iMac after i download the bwa-0.6.1.tar.bz2 file. I know that i should do that using the terminal window but I am not sure how to do it. Any help?

Last edited by MMPE; 12-05-2011 at 03:12 AM.
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Old 12-05-2011, 05:25 AM   #2
kga1978
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You need to have Xcode from Apple installed (can be found on the AppStore). Extract the bwa archive and cd into it from the terminal. Then simply type `make' to compile and copy the resulting executable `bwa' anywhere you want (I would put it under /usr/local/bin - e.g sudo mv bwa /usr/local/bin).
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Old 12-05-2011, 09:09 PM   #3
Jon_Keats
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Take a look at this thread (http://seqanswers.com/forums/showthread.php?t=4589). Shameless plug as it is my own but it should help get you going. Sadly bwa will be just the start...
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Old 05-04-2012, 05:34 PM   #4
yehudithasin
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Hi
About bwa and Mac.....I am trying to install bwa on Mac, after upgrading to Lion (I already downloaded the xcode 4 and added the relevant library to PATH). After trying 'make' I get the following message:

"gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
QSufSort.c:32:19: error: stdio.h: No such file or directory
QSufSort.c:33:20: error: stdlib.h: No such file or directory
In file included from QSufSort.c:34:
/Developer/usr/bin/../lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:10:25: error: limits.h: No such file or directory
make: *** [QSufSort.o] Error 1"


I have no idea what that error means and how to fix it.....any suggestions please?
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Old 05-05-2012, 12:02 AM   #5
Jon_Keats
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Unfortunately Apple no longer packages the gcc compiler as part of the Xcode4 package that works with Mac OS Lion. To get around this issue you can install MacPorts and the gcc4.2 compiler package.

Another option is in this thread:
http://stackoverflow.com/questions/5...ort-to-xcode-4
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Old 05-05-2012, 09:56 AM   #6
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Quote:
Originally Posted by Jon_Keats View Post
Unfortunately Apple no longer packages the gcc compiler as part of the Xcode4 package that works with Mac OS Lion. To get around this issue you can install MacPorts and the gcc4.2 compiler package.

Another option is in this thread:
http://stackoverflow.com/questions/5...ort-to-xcode-4
It works for me. Another thread though:
http://superuser.com/questions/31310...ion-delete-gcc
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Old 05-07-2012, 10:19 AM   #7
yehudithasin
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Thanks, installing the command line tools worked for me, although ad to go to developer site (https://developer.apple.com/downloads/). Installation from Xcode failed at checksum
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Old 08-04-2012, 10:23 PM   #8
vandy
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hello there,

I am very new to this and this is my first post. so please bear a bit with me.

I am facing problem in installing bwa on my laptop. I have installed Xcode and then downloaded bwa-0.6.2 version on my Mac OS X ver 10.7.4. whenever i type make to execute its giving me an error.

-bash: make: command not found

Any suggestion
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Old 08-04-2012, 11:06 PM   #9
Jon_Keats
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Try the following:

You need to install Xcode from App Store: http://itunes.apple.com/us/app/xcode/id448457090?mt=12

Then start Xcode, go to Xcode->Preferences->Downloads and install component named "Command Line Tools". After that all the relevant tools will be placed in /usr/bin folder and you will be able to use it just as it was in 10.6
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Old 08-05-2012, 11:59 PM   #10
vandy
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Thank you Jon_Keats.
I did download xcode as per your suggestion. It worked this time.
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Old 10-24-2013, 06:45 AM   #11
maivantan
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Hi all,
I am a new bioinoformatic field.
I want to install BWA. I already installed Xcode. However, I could not install BWA.
I type 'make' in terminal but can not success
Any suggestion in detail please
thank you very much
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Old 06-02-2015, 05:56 AM   #12
gsr9999
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thanks for the post, I installed the gcc on my mac 10.9.5 with the following command

xcode-select --install
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