Question: deeptools installation on MacBook
0
gravatar for BioDH
2.7 years ago by
BioDH0
BioDH0 wrote:

I'm trying install deeptools on my Mac.

I did.

~ pip install --user deeptools

Requirement already satisfied: deeptools in ./Library/Python/2.7/lib/python/site-packages
Requirement already satisfied: numpy>=1.9.0 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: scipy>=0.17.0 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: matplotlib>=1.4.0 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: pysam>=0.8.2 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: numpydoc>=0.5 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: pyBigWig>=0.2.1 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: py2bit>=0.2.0 in ./Library/Python/2.7/lib/python/site-packages (from deeptools)
Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.4.0->deeptools)
Requirement already satisfied: functools32 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib>=1.4.0->deeptools)
Requirement already satisfied: pytz in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.4.0->deeptools)
Requirement already satisfied: six>=1.10 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib>=1.4.0->deeptools)
Requirement already satisfied: cycler>=0.10 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib>=1.4.0->deeptools)
Requirement already satisfied: subprocess32 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib>=1.4.0->deeptools)
Requirement already satisfied: python-dateutil in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.4.0->deeptools)
~

But If type "bamCoverage"

~ bamCoverage

-bash: bamCoverage: command not found

~ deeptools

-bash: deeptools: command not found

How can I use deeptools.

What's wrong with deeptools

install deeptools mac • 1.5k views
ADD COMMENTlink modified 2.5 years ago by inowkeren0 • written 2.7 years ago by BioDH0
0
gravatar for genomax
2.7 years ago by
genomax75k
United States
genomax75k wrote:

Depending where deepTools was installed you may need to add that directory to your $PATH in order to be directly able to run the program: http://unix.stackexchange.com/questions/183295/adding-programs-to-path

That location may be $HOME/.local/bin/ (since you did not specify a location during install). If $HOME/.local/bin/bamCoverage --help produces a help output add $HOME/.local/bin/ directory to your $PATH.

ADD COMMENTlink modified 2.7 years ago by Devon Ryan93k • written 2.7 years ago by genomax75k
0
gravatar for inowkeren
2.5 years ago by
inowkeren0
inowkeren0 wrote:

assuming there is a deepTools folder in your home folder, in the terminal: export path=~/deepTools/bin:$path

thanks

ADD COMMENTlink written 2.5 years ago by inowkeren0
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