Installing anvi'o on UBUNTU 14.04

[owenoutlaw]

Greetings,

I am trying to install anvi'o on Ubuntu 14.04. All dependencies look good (except MyRAST--could not get that working). This is the terminal output when I try to install running sudo pip install anvio

$ sudo pip install anvio
(...)
    x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.7/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
    In file included from samtools/bam.h:48:0,
                     from samtools/sam.h:29,
                     from pysam/csamtools.c:250:
    htslib/htslib/bgzf.h:34:18: fatal error: zlib.h: No such file or directory
     #include <zlib.h>
                      ^
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

[ozcan]

Hello, zlib1g-dev package provides missing zlib.h file, you can install it via apt-get.

Thanks for the feedback, i am going to try to installing anvio on a clean ubuntu installation to check any possible installation problems.

[owenoutlaw]

Hello,

Thanks. that partly worked. I should also mention that this is a fresh install of Ubuntu. Anvi'o is the first program I am installing

$  sudo pip install anvio
(...)
_get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/linalg/setup.py", line 19, in configuration
        raise NotFoundError('no lapack/blas resources found')
    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    ----------------------------------------
  Rolling back uninstall of scipy
Command "/usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-jAUmwE/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ZRyhYd-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-jAUmwE/scipy

[meren]

Hi @owenoutlaw,

It seems libblas-dev liblapack-dev packages need to be installed with apt-get.

@ozcanesen, I think a step by step installation manual on a fresh Ubuntu system is going to be necessary.

Maybe a docker image would be the best solution for most?

[owenoutlaw]

This took care of a few issues but this is the current terminal output. I have searched around and tried a few fixes but none work

(...)
    ./anvio/extensions/concoct/c_vbgmm_fit.c:14:28: fatal error: gsl/gsl_vector.h: No such file or directory
     #include <gsl/gsl_vector.h>
                                ^
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

[owenoutlaw]

Ok--looks like installation was successful with the following. I will run the mini-test. Thanks for the help apt-get install gsl-bin apt-get install libgsl0-dbg apt-get install libgsl0-dev apt-get install libgsl0ldbl

[meren]

Great to hear, @owenoutlaw. Thank you for helping us. It would be very helpful if you could copy-paste all the apt-get operations you needed to perform before the successful pip install step here.

You can simply run this command, and send here the output:

history | grep apt-get | sort | uniq

Thank you very much in advance!

[owenoutlaw]

works like a charm now. Thank you for the great programs! here are the apt-get ops.

sudo apt-get install build-essential
sudo apt-get install gcc
sudo apt-get install gsl
sudo apt-get install gsl-bin
sudo apt-get install libblas-dev
sudo apt-get install libevent-dev
sudo apt-get install libgsl0-dbg
sudo apt-get install libgsl0-dev
sudo apt-get install libgsl0ldbl
sudo apt-get install liblapack-dev
sudo apt-get install libxml2-dev
sudo apt-get install libxslt
sudo apt-get install libxslt1-dev
sudo apt-get install python-dev
sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
sudo apt-get install python-setuptools
sudo apt-get install python-twisted-web python2.7-dev
sudo apt-get install sql
sudo apt-get install zlib1g-dev

[owenoutlaw]

FYI--I tried to reinstall and all looks good except it no longer produces an HTML file and the last line of the output on minitest reads:

./run_mini_test.sh: line 101: anvi-get-short-reads-from-bam: command not found

[meren]

That is normal, @owenoutlaw. Probably you are using the latest codebase to run the mini test, but when you type anvi-profile --version you would see 1.0.0. So the tests are a bit further than your installation :)

[lstavr]

Thank you @owenoutlaw