installation problems

[mforde84]

I'm looking for some clarification on installing BreaKmer.

After running the setup script, a egg is generated in site packages which generates the following error:

python: can't find 'main' module in '/path/to/egg/pysam-0.14-py2.7-linux-x86_64.egg'

Also the "breakmer.py" script found in the root github directory generates the following error:

$ python breakmer.py
Traceback (most recent call last): File "breakmer.py", line 5, in import breakmer.params as params File "/home/blik/Desktop/ccgd-profile-BreaKmer-3a38315/breakmer/params.py", line 12, in import breakmer.utils as utils File "/home/blik/Desktop/ccgd-profile-BreaKmer-3a38315/breakmer/utils.py", line 12, in from pysam import * AttributeError: 'module' object has no attribute 'TupleProxy'

Can you please clarify how to install and run BreaKer please.

[jacquayj]

Hey @mforde84,

I figured out how to get past these issues on my MacOS 10.13.6 system. Just checkout the commit e9effd2. The setup.py needed a few updates for a specific pysam version and a missing matplotlib dependency.

Here are complete instructions:

• Install latest python2.7 release
• Install virtualenv pip2.7 install virtualenv
• Clone repo git clone git@github.com:ccgd-profile/BreaKmer.git
• cd BreaKmer
• Checkout my branch git checkout e9effd2
• python2.7 -m virtualenv env
• source env/bin/activate
• python2.7 setup.py install

And run:

python2.7 breakmer.py

Edit: It looks like the master branch is unstable, you may want to use Breakmer_0.0.6_Profile_CCGDProduction branch instead.