Linux Anaconda 4.1.0 64bit circos install about network-analysis-made-simple HOT 5 CLOSED

Hi @NeonGoby, thanks for posting! There's an alternate way of checking whether you have Circos installed properly - in a Python REPL, can you import circos? If you get an IPython.kernel error, just ignore it; I'm just trying to make sure you don't encounter the ImportError: No module named 'circos' .

As an alternate way of checking, can you try running all of Notebook 2 (Instructor version)? If you have no errors in there, you're also good to go.

If you have errors, please post them, and let me know!

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Hi Eric,

pip install put the following files in to the site-packages folder:

~/anaconda3/lib/python3.5/site-packages/Circos-1.1.dist-info $ lltotal 48

drwxr-xr-x 2 jh jh 4096 Jul 2 22:30 ./
drwxr-xr-x 202 jh jh 16384 Jul 2 22:30 ../
-rw-r--r-- 1 jh jh 77 Jul 2 22:30 DESCRIPTION.rst
-rw-r--r-- 1 jh jh 4 Jul 2 22:30 INSTALLER
-rw-r--r-- 1 jh jh 435 Jul 2 22:30 METADATA
-rw-r--r-- 1 jh jh 568 Jul 2 22:30 metadata.json
-rw-r--r-- 1 jh jh 630 Jul 2 22:30 RECORD
-rw-r--r-- 1 jh jh 1 Jul 2 22:30 top_level.txt
-rw-r--r-- 1 jh jh 92 Jul 2 22:30 WHEEL

These looks too small to be a full package.

I did an anaconda search -t circosand it found a bioconda/circos package
that I installed via:

conda install --channel https://conda.anaconda.org/bioconda circos

That install some perl script as well as a circos executable.

Even then I still cannot import circos

On 07/02/2016 04:17 PM, Eric Ma wrote:

Hi @NeonGoby https://github.com/NeonGoby, thanks for posting!
There's an alternate way of checking whether you have Circos installed
properly - in a Python REPL, can you |import circos|? If you get an
IPython.kernel error, just ignore it; I'm just trying to make sure you
don't encounter the |ImportError: No module named 'circos'
|.

As an alternate way of checking, can you try running all of Notebook 2
(Instructor version)? If you have no errors in there, you're also good
to go.

If you have errors, please post them, and let me know!

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I think I get what happened! This is definitely my fault, I fixed the setup.py script in my Circos GitHub repository, but forgot to upload it to PyPI.

Can you do the following:

1. Uninstall the conda Circos (I'm not one of the maintainers of the bioconda channel, so I'm not sure what that package is). The command is likely conda remove circos.
2. In case something is still lingering around, do pip uninstall circos as well.
3. Finally, install Circos from GitHub directly: pip install git+https://github.com/ericmjl/Circos.git.

Let me know if this works out! I will also upload a new version of Circos to PyPI.

Thanks for catching this for us, much appreciated!

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FWIW, I just uploaded Circos 1.2 to PyPI, which fixes the installation issue. I should really setup continuous integration on Circos, to ensure that pip-based installation works.

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Thanks the install from your github did the trick, the notebook 2
instructor ran successfully.

Thank you very much, looking forward to next week.

On 07/03/2016 06:06 AM, Eric Ma wrote:

|pip install git+https://github.com/ericmjl/Circos.git|

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