libBioLCCC installation problems

[Achim]

Dear team at BioLCCC,

first of all many thanks for providing a very exciting tool to the
scientific community. I particularly like it that you have given it a
python wrapper, to make interaction with the library a bit easier for
people like myself who are computationally possibly a bit challenged.

I have downloaded libbiolccc and pyteomics to my ubuntu Lucid Lynx
box. I have unpacked them into a directory within my home directory
(could also put it anywhere else, if that is better). Within the same
directory I have put another directory called 'build'. When I try to
compile libbiolccc with the command

> scons -Y ~/BioLCCC/libbiolccc/ all

scons terminates with the following error message:

mkdir ./doc/sphinx/source/examples; cp src/examples/*.py ./doc/sphinx/
source/examples; cp src/examples/*.cpp ./doc/sphinx/source/examples;
cd ./doc/sphinx; make html; cd ../
sphinx-build -b html -d build/doctrees source build/html
Traceback (most recent call last):
File "/usr/local/bin/sphinx-build", line 9, in <module>
load_entry_point('Sphinx==1.0.7', 'console_scripts', 'sphinx-
build')()
File "/usr/lib/python2.6/dist-packages/pkg_resources.py", line 299,
in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/lib/python2.6/dist-packages/pkg_resources.py", line 2228,
in load_entry_point
raise ImportError("Entry point %r not found" % ((group,name),))
ImportError: Entry point ('console_scripts', 'sphinx-build') not found
make: *** [html] Error 1
mv doc/sphinx/build/html/* doc/
mv: cannot stat `doc/sphinx/build/html/*': No such file or directory
scons: *** [docs] Error 1
scons: building terminated because of errors.

Any idea where I am going wrong?

Many thanks for your support,
Achim

[Anton Goloborodko]

Dear Achim,

thank you for your interest in BioLCCC! We really appreciate your
feedback and will find the source of the problem you have experienced.

Meanwhile, if you just plan to invoke libBioLCCC from python, you can
install pyBioLCCC library using a much simplier routine described in
http://theorchromo.ru/lib/build.html#installing-pybiolccc-from-pypi .

Briefly, print the following commands in the system command line:
sudo apt-get install python-setuptools
sudo easy_install pip
sudo pip install pyBioLCCC

The first two commands will install easy_install and pip python
package managers. With the third command you will download and compile
the latest version of pyBioLCCC.

Please, do not hesitate to contact us if you have further questions.

Sincerely yours,
Anton Goloborodko,
Research Assistant,
INEPCP, Russian Academy of Sciences.

[Achim]

Dear Anton,

many thanks for your support! This is to summarise for the benefit of
the community and of search engines several useful bits of advice that
you gave me get pyBioLCCC running on my ubuntu Lucid Lynx box.

First of all, I was not aware that pyBioLCCC on its own is entirely
sufficient to obtain al lthe functionality of the BioLCCC modules. The
C++ libraries are essential only for those, who really want to dive
into that bit of code. As a user, I only needed the pyBioLCCC
installation.

Using easy_install and pip, as outlined in the instructions
http://theorchromo.ru/lib/build.html#installing-pybiolccc-from-pypi

I installed the libraries. Following installation, I needed to change
permissions for the library in the following directory:
/usr/local/lib/python2.6/dist-packages/

using the command
sudo chmod ugo+r /usr/local/lib/python2.6/dist-packages/*pyBioLCCC*

This was only necessary on one of my Linux computers, on a different
one (running ubuntu 11.04 'Natty Narwhal'), the installation went fine
without problems.

Many thanks again,
Achim

On Jul 14, 7:39 pm, Anton Goloborodko <goloborodko.an...@gmail.com>
wrote:

> Dear Achim,
>
> thank you for your interest in BioLCCC! We really appreciate your
> feedback and will find the source of the problem you have experienced.
>
> Meanwhile, if you just plan to invoke libBioLCCC from python, you can

> install pyBioLCCC library using a much simplier routine described inhttp://theorchromo.ru/lib/build.html#installing-pybiolccc-from-pypi .

>
> Briefly, print the following commands in the system command line:
> sudo apt-get install python-setuptools
> sudo easy_install pip
> sudo pip install pyBioLCCC
>
> The first two commands will install easy_install and pip python
> package managers. With the third command you will download and compile
> the latest version of pyBioLCCC.
>
> Please, do not hesitate to contact us if you have further questions.
>
> Sincerely yours,
> Anton Goloborodko,
> Research Assistant,
> INEPCP, Russian Academy of Sciences.
>