libbz2.so.1.0 cannot open shared object file

[simoncchu]

I met an issue after finished installing nucleus using command (no error happens):
pip install --user google-nucleus

However, when I try to run the following demo code, I got error:

from nucleus.io import vcf
sf_vcf="test_nist.b37_chr20_100kbp_at_10mb.vcf.gz"
with vcf.VcfReader(sf_vcf) as reader:
    print('Sample names in VCF: ', ' '.join(reader.header.sample_names))

libbz2.so.1.0: cannot open shared object file: No such file or directory

Any suggestion for solving the issue? Thank you!

[ThomasColthurst]

One easy suggestion is to try running the demo code from a different directory. This error can happen if you run the demo from the Nucleus base directory, because then Python tries to load Nucleus from that location rather than from the installed location, and only the installed location has the compiled .so files.

If that doesn't work, you will want to run
$ python

import sys
sys.path
to see where Python is importing Nucleus from. (Since you used --user, the directory name will probably be based in your home directory and will include "site-packages" at the end.)

Once you have that directory, run
$ ls [import dir]/nucleus/io/python

That directory should contain a bunch of .so files like bedgraph_reader.so, gff_writer.so, etc. If it doesn't, there was an installation error.

[simoncchu]

I run outside the installation folder, but still got the error.

run sys.path I got:

['', '/user_path/anaconda2/lib/python27.zip', '/user_path/anaconda2/lib/python2.7', '/user_path/anaconda2/lib/python2.7/plat-linux2', '/user_path/anaconda2/lib/python2.7/lib-tk', '/user_path/anaconda2/lib/python2.7/lib-old', '/user_path/anaconda2/lib/python2.7/lib-dynload', '/user_path/.local/lib/python2.7/site-packages', '/user_path/anaconda2/lib/python2.7/site-packages', '/user_path/anaconda2/lib/python2.7/site-packages/Sphinx-1.5.6-py2.7.egg', '/user_path/anaconda2/lib/python2.7/site-packages/matplotlib_venn-0.11.5-py2.7.egg']

I saw the .so files under /user_path/.local/lib/python2.7/site-packages:

bedgraph_reader.so  bed_writer.so    gff_reader.so            __init__.py                reference.so   unindexed_fasta_reader.so
bedgraph_writer.so  fastq_reader.so  gff_writer.so            __init__.pyc               sam_reader.so  vcf_reader.so
bed_reader.so       fastq_writer.so  indexed_fasta_reader.so  in_memory_fasta_reader.so  sam_writer.so  vcf_writer.so

[pgrosu]

Just update your LD_LIBRARY_PATH and PYTHONPATH environmental variables, and try again.

[simoncchu]

Sorry @pgrosu, how do I update?

[pgrosu]

Here are a few links describing it for LD_LIBRARY_PATH:

https://www.tecmint.com/understanding-shared-libraries-in-linux/
https://docs.oracle.com/cd/E19455-01/816-0559/chapter2-48927/index.html

The same for PYTHONPATH, which is described here:

https://docs.python.org/2/using/cmdline.html#envvar-PYTHONPATH

Make sure you echo them out for (i.e. echo $LD_LIBRARY_PATH) to see what they already contain, which you want to keep. You can test changes like this:

LD_LIBRARY_PATH=your_DIR:$LD_LIBRARY_PATH PYTHONPATH=... python Your_Program ...

Basically standard Linux config :)

~p

[simoncchu]

Problem for me is I don't know where libbz2.so.1.0 is? @pgrosu

[pgrosu]

@ReedWarbler Which linux distribution do you have (i.e. Ubuntu, Redhat, etc)? I can point you to where you can get the package for it from. Alternatively, you can compile it from source, which you can get it from here:

https://sourceforge.net/projects/bzip2/files/

[xyq013563]

Here are a few links describing it for LD_LIBRARY_PATH:

https://www.tecmint.com/understanding-shared-libraries-in-linux/
https://docs.oracle.com/cd/E19455-01/816-0559/chapter2-48927/index.html

The same for PYTHONPATH, which is described here:

https://docs.python.org/2/using/cmdline.html#envvar-PYTHONPATH

Make sure you echo them out for (i.e. echo $LD_LIBRARY_PATH) to see what they already contain, which you want to keep. You can test changes like this:

LD_LIBRARY_PATH=your_DIR:$LD_LIBRARY_PATH PYTHONPATH=... python Your_Program ...

Basically standard Linux config :)

~p

Thank you very much! Update the LD_LIBRARY_PATH definitely fixed all of my problems.

[pgrosu]

You're very welcome @xyq013563!
~p