Installation of Burrows-Wheeler Alignment Tool (bwa) on Mac

[MMPE]

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?

[kga1978]

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).

[Jon_Keats]

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...

[yehudithasin]

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?

[Jon_Keats]

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/5333490/how-can-we-restore-ppc-ppc64-as-well-as-full-10-4-10-5-sdk-support-to-xcode-4

[nilshomer]

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/313107/does-updating-to-os-x-lion-delete-gcc

[yehudithasin]

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

[vandy]

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

[Jon_Keats]

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

[vandy]

Thank you Jon_Keats.
I did download xcode as per your suggestion. It worked this time.

[maivantan]

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

[gsr9999]

jon keats and nils homer, Thank You for your answers for this post.

I followed nilshomer's posted link and tried to do what the following , what <jbm hack> posted : <Preferences --> Downloads --> Command Line Tools, and click on installWith "Components">. But this didn't work for me.

So, I rather followed the instruction in this post http://apple.stackexchange.com/quest...oads-for-devel

And then I ran the following command :

$xcode-select --install

This above command worked for me and the c++ compiler gcc got installed successfully on my mac 10.9.5. And I am now able to compile the bwa

[gsr9999]

thanks for the post, I installed the gcc on my mac 10.9.5 with the following command

xcode-select --install