Install Lefse in Ubuntu 12

Question

[goh]

Hi all,

I'm new to bioinformatics and command/ scripts.

I have been trying to install lefse in ubuntu 12 which i build in virtualbox, but unsuccessful.

I have found and followed one instructions as below. https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial

However, still couldn't manage to get the package installed. Do i need to execute other scripts or install other packages besides the one listed required by lefse to run ?

Does anyone faced similar problems before?

Thanks.

Regards, Goh.

[WouterDeCoster]

Any reason you installed Ubuntu 12? That's 6 years old...

However, still couldn't manage to get the package installed.

Does anyone faced similar problems before?

Please elaborate on error messages/output/reason why you believe the package is not installed. We cannot see what happens on your computer so you'll have to be more precise.

[goh]

i have successfully installed pip and matplotlib using the command as below.

sudo apt-get python-pip
sudo apt-get python-matplotlib

When i execute the command below i have these errors

 sudo pip install https://bitbucket.org/nsegata/lefse/get/default.zip
Downloading/unpacking https://bitbucket.org/nsegata/lefse/get/default.zip
  Downloading default.zip (61Kb): 61Kb downloaded
  Running setup.py egg_info for package from https://bitbucket.org/nsegata/lefse/get/default.zip
    Traceback (most recent call last):
      File "<string>", line 14, in <module>
    IOError: [Errno 2] No such file or directory: '/tmp/pip-ZPkYIX-build/setup.py'
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 14, in <module>

IOError: [Errno 2] No such file or directory: '/tmp/pip-ZPkYIX-build/setup.py'

----------------------------------------
Command python setup.py egg_info failed with error code 1

Fyi, i have just installed ubuntu 12 in virtual box and im using windows. Could you please advice ?

Thanks. Goh.

[Bastien Hervé]

Try to :

pip install --upgrade pip

From here and there

And retry your python setup

[goh]

Hi,

Do you mean the Ubuntu setup from the begining?

Regards, Goh

[Bastien Hervé]

No, do :

pip install --upgrade pip
sudo pip install https://bitbucket.org/nsegata/lefse/get/default.zip

[goh]

Hi, pip install --upgrade pip resulted some error as below. Btw, im now using ubuntu 14.

luc@luc-VirtualBox:~$ pip install --upgrade pip
Downloading/unpacking pip from https://files.pythonhosted.org/packages/0f/74/ecd13431bcc456ed390b44c8a6e917c1820365cbebcb6a8974d1cd045ab4/pip-10.0.1-py2.py3-none-any.whl#sha256=717cdffb2833be8409433a93746744b59505f42146e8d37de6c62b430e25d6d7
  Downloading pip-10.0.1-py2.py3-none-any.whl (1.3MB): 1.3MB downloaded
Installing collected packages: pip
  Found existing installation: pip 1.5.4
    Not uninstalling pip at /usr/lib/python2.7/dist-packages, owned by OS
  Can't roll back pip; was not uninstalled
Cleaning up...
Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 122, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 283, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1436, in install
    requirement.install(install_options, global_options, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 672, in install
    self.move_wheel_files(self.source_dir, root=root)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 902, in move_wheel_files
    pycompile=self.pycompile,
  File "/usr/lib/python2.7/dist-packages/pip/wheel.py", line 206, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/lib/python2.7/dist-packages/pip/wheel.py", line 193, in clobber
    os.makedirs(destsubdir)
  File "/usr/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/pip-10.0.1.dist-info'

[WouterDeCoster]

Btw, im now using ubuntu 14.

Interesting step forward. Only a couple more version to go and you are current.

[GenoMax]

Hello goh ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[GenoMax]

goh : Try adding sudo before your upgrade command.

[Bastien Hervé]

But... why 14 ?

Also, this "error" is well known over the web, just try to google your program name + your error like pip install [Errno 13] Permission denied.

First link

First answer -> Have you tried with sudo?

[goh]

Hi i tried two command:-

sudo pip install https://bitbucket.org/nsegata/lefse/get/default.zip
sudo -H pip install https://bitbucket.org/nsegata/lefse/get/default.zip

Both failed with error msg,

Could not install packages due to an environment error

Than i downloaded the zip file an unzipped. Trying to install from local. Using the command below:-

sudo -H pip install 'myfilepath/lefse.py'

The error said invalid requirement:  'myfilepath/lefse.py'
It looks like a path. It does exist.

~ Tried the fix as suggested previous post

there is no such file or directory

Any idea ? Thanks.

I'm using ubuntu 16, and probably gonna use it for some time as i did not see any 32bit desktop iso file in 17 n 18.

[Bastien Hervé]

The two commands were :

sudo pip install --upgrade pip
sudo pip install https://bitbucket.org/nsegata/lefse/get/default.zip

Did you do the first one ?

If you got this error :

Could not install packages due to an EnvironmentError:

[Errno 13] Permission denied:

The important information is [Errno 13] Permission denied:

Why select a 32bits version ? The only reason I found to take a 32bits version is that a software required it.

[goh]

Hi,

Because I read some where that LEfSe scripts require python2, and rpy2 to communicate with R, but the newest releases of rpy2 no longer support python2 - only python3.

As I'm very new in this, so I choose the earliest Ubuntu version. Because I think python version comes with the Ubuntu installation together. Please correct me if I'm wrong. Thanks.

Goh.

[Bastien Hervé]

You can set up the python version you want on the Ubuntu version you want, python version is not correlated with Ubuntu version. I think you missunderstood with the ubuntu repo.

You can also setup two different versions of python on the same Ubuntu (like python 2.7 and 3.5 on Ubuntu 16.04, what I have).

In rpy2 requirements you can get :

Python -> 3.5, with intended compatibility with 2.7 and >3.3

IMO, install Ubuntu 16.04 with python 2.7 and that will be OK

[Bastien Hervé]

Prerequisites for your program are here : https://bitbucket.org/nsegata/metaphlan/overview

• MetaPhlAn requires python 2.7 or higher with argparse, tempfile and numpy libraries installed (apart for numpy they are usually installed together with the python distribution). Python3 is not supported yet.

• If you provide the output of BLASTN or BowTie2 as input, there are no additional prerequisite.

• If you would like to use the integrated BLASTN in MetaPhlAn, you need to have: blastn from the NCBI BLAST+ package version 2.2.25 or higher (blastn needs to be in the system path)

• If you would like to use the BowTie2 integrated in MetaPhlAn, you need to have: BowTie2 version 2.0.0 or higher and perl (bowtie2 needs to be in the system path with execute _and_ read permission)