installation about macs

[xiaomimeow]

Sorry figured it out.

[dfv]

@xiaomimeow Hey can you please tell me how this error got solved beacuse I am also getting same error.

Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 55, in main
from MACS2.callpeak import run
ImportError: No module named MACS2.callpeak

Thanks a lot

Ankit

[bgruening]

Can you check if macs2 is in your python path? If not please add the entire path to macs2 into your python path.

[dfv]

Thanks a lot for replying! I have checked macs2 is already there in my python path! I have also mentioned the path through:
export PYTHONPATH
export PATH

Thanks

[dfv]

Is there any possibility what went wrong in it?

[taoliu]

Could you share us how you installed MACS, in detail?

Tao

On Feb 17, 2014, at 8:32 AM, dfv [email protected] wrote:

Is there any possibility what went wrong in it?

—
Reply to this email directly or view it on GitHub.

[dfv]

Hi Tao,
I have installed python 2.7.2 locally and numpy 1.8.0 in python directory. In accordance to it seperately i have installed macs2 as mentioned in instrutions with help of python setup.py install command. But when i try to run macs2 with the help of below command :

./macs2 callpeak -t abc.bam -c xyz.bam -f BAM -g ce --broad -n test

I get this error
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 40, in main
argparser = prepare_argparser()
File "./macs2", line 109, in prepare_argparser
argparser.add_argument("--version", action="version", version="%(prog)s" +MACS_VERSION)
NameError: global name 'MACS_VERSION' is not defined

and after uncommenting MACS_VERSION in script then I get error mentioned below:
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 55, in main
from MACS2.callpeak import run
ImportError: No module named MACS2.callpeak

Thanks a lot

[taoliu]

Hi dfv,

If you install MACS2 using setup script, then I don't understand why you still need to type './macs2' to run it. The executable 'macs2' script should be installed into /usr/local/bin in linux or Mac OSX by default, and the path (e.g. /usr/local/bin) should be in your environment variable 'PATH'. After installation, you should LEAVE the source code directory, and you shouldn't run './macs2' there.

Best,
Tao

On Feb 17, 2014, at 11:36 AM, dfv [email protected] wrote:

Hi Tao,
I have installed python 2.7.2 locally and numpy 1.8.0 in python directory. In accordance to it seperately i have installed macs2 as mentioned in instrutions with help of python setup.py install command. But when i try to run macs2 with the help of below command :

./macs2 callpeak -t abc.bam -c xyz.bam -f BAM -g ce --broad -n test

I get this error
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 40, in main
argparser = prepare_argparser()
File "./macs2", line 109, in prepare_argparser
argparser.add_argument("--version", action="version", version="%(prog)s" +MACS_VERSION)
NameError: global name 'MACS_VERSION' is not defined

and after uncommenting MACS_VERSION in script then I get error mentioned below:
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 55, in main
from MACS2.callpeak import run
ImportError: No module named MACS2.callpeak

Thanks a lot

[dfv]

Hi Tao,
Thank you so much it solved!