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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Install problems (again) #209

Closed jcthrash closed 8 years ago

jcthrash commented 8 years ago

Hello, I'm sorry to trouble you again, but after returning to work with Anvi'o today, the previous installation is not letting me complete tasks any longer.

As of our last outing, you had me complete the following:

cd /tmp
git clone -b v1.2.0  --depth=1 https://github.com/meren/anvio.git
cd anvio/tests
./run_mini_test

When I looked in /tmp today, anvio was no longer there, so I re-installed it in this way, but received the following output 

$ ./run_mini_test.sh 

#
#
# Creating the output directory ...
#
#

#
#
# Anvo'o version ...
#
#

./run_mini_test.sh: line 12: anvi-profile: command not found

It doesn't work with sudo either.

I removed the /tmp/anvio directory and attempted to install in /usr/local/bin, where I usually put tools of this nature.

$ sudo pip install anvio
The directory '/Users/JCThrash/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/JCThrash/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Requirement already satisfied (use --upgrade to upgrade): anvio in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): bottle>=0.12.7 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): pysam>=0.8.3 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): hcluster>=0.2.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): ete2>=2.2 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): scipy in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): scikit-learn>=0.15 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): django>=1.7 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): cython>=0.21a1 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): h5py>=2.5.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from anvio)
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.6.1 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from h5py>=2.5.0->anvio)
Requirement already satisfied (use --upgrade to upgrade): six in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from h5py>=2.5.0->anvil)

This appears to indicate I have everything installed, but I don't know what directory it is in. There is no anvio directory in /usr/local/bin, nor in /opt/local/bin where macports has been putting everything.

Can you help me get back on track?

Thank you.

meren commented 8 years ago

Hi Cameron,

I am sorry for confusing you. What we did under the /tmp directory was simply to run mini_test. So you had anvi'o installed, and then you downloaded a copy of the codebase somewhere public just to run the mini_test with your installed anvi'o. It is OK for everything under the /tmp to be gone.

Your installation is still there. It is again the PATH problem we are facing here. When you type any anvio program your terminal tells you it is not there, because your PATH does not include the directory where your Python binaries reside.

Please paste these lines into your terminal:

echo 'export PATH=$PATH:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin' >> ~/.bashrc
source ~/.bashrc

Then everything will magically work (including the mini_test).

If you run into similar issues, please send me a direct e-mail (a.murat.eren gmail), if we identify a problem we can open an issue to get them fixed :)

I hope anvi'o would prove useful to you after all these trouble it caused you.

Best,