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Installing Qiime on Ubuntu

I am a new to this field and trying to install QIIME to a ubuntuserver where I need to use the scripts to build a simple web-based app for a class assignment. I use http://qiime.org/1.8.0/install/install.html to do the base installation using pip. I tried to install pip using

sudo apt-get install python-pip​

and got this error

Err http://us.archive.ubuntu.com/ubuntu/ raring/main dpkg-dev all 1.16.10ubuntu1
  404  Not Found [IP: 91.189.91.14 80]
Err http://us.archive.ubuntu.com/ubuntu/ raring/main build-essential i386 11.6ubuntu4
  404  Not Found [IP: 91.189.91.14 80]
Err http://us.archive.ubuntu.com/ubuntu/ raring/main fakeroot i386 1.18.4-2ubuntu1
  404  Not Found [IP: 91.189.91.14 80]
Err http://us.archive.ubuntu.com/ubuntu/ raring/main libalgorithm-diff-xs-perl i386 0.04-2build3
  404  Not Found [IP: 91.189.91.14 80]
Err http://us.archive.ubuntu.com/ubuntu/ raring/main python-setuptools all 0.6.34-0ubuntu1
  404  Not Found [IP: 91.189.91.14 80]
Err http://us.archive.ubuntu.com/ubuntu/ raring/universe python-pip all 1.3.1-0ubuntu1
  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/g/gcc-4.7/libstdc++6-4.7-dev_4.7.3-1ubuntu1_i386.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/g/gcc-4.7/g++-4.7_4.7.3-1ubuntu1_i386.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/g/gcc-defaults/g++_4.7.3-1ubuntu10_i386.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/d/dpkg/dpkg-dev_1.16.10ubuntu1_all.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/b/build-essential/build-essential_11.6ubuntu4_i386.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/f/fakeroot/fakeroot_1.18.4-2ubuntu1_i386.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/liba/libalgorithm-diff-xs-perl/libalgorithm-diff-xs-perl_0.04-2build3_i386.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/main/d/distribute/python-setuptools_0.6.34-0ubuntu1_all.deb  404  Not Found [IP: 91.189.91.14 80]
Failed to fetch http://us.archive.ubuntu.com/ubuntu/pool/universe/p/python-pip/python-pip_1.3.1-0ubuntu1_all.deb  404  Not Found [IP: 91.189.91.14 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

Should I use qiime deploy instead? I tried to follow https://github.com/qiime/qiime-deploy

But I don't really understand how it works and not sure with the version of my Ubuntu.

UPDATE: I tried to follow http://qiime.org/1.8.0/install/install.html on my machine with ubuntu 14.04 virtual machine and working internet. I installed pip and ran

sudo apt-get install build-essential

and

pip install numpy==1.7.1

but got this error

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 1431, in install
    requirement.uninstall(auto_confirm=True)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 598, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1836, in remove
    renames(path, new_path)
  File "/usr/lib/python2.7/dist-packages/pip/util.py", line 295, in renames
    shutil.move(old, new)
  File "/usr/lib/python2.7/shutil.py", line 303, in move
    os.unlink(src)
OSError: [Errno 13] Permission denied: '/usr/local/bin/f2py'

Traceback (most recent call last):
  File "/usr/local/bin/pip", line 9, in <module>
    load_entry_point('pip==1.5.4', 'console_scripts', 'pip')()
  File "/usr/lib/python2.7/dist-packages/pip/__init__.py", line 235, in main
    return command.main(cmd_args)
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 161, in main
    text = '\n'.join(complete_log)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 72: ordinal not in range(128)

Should I continue with

pip install qiime
metagenomics qiime
• 7,639 views • link
updated by Ram Ram • written by weiven90 • weiven90

Did you do sudo apt-get update before installing?

• 0 views • link
updated by Ram Ram • written by venu venu

Yes and these are the last several lines of error.

W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring/multiverse/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/main/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/restricted/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/universe/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/multiverse/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/main/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/restricted/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/universe/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-updates/multiverse/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/main/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/restricted/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/universe/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/multiverse/source/Sources  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/main/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/restricted/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/universe/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/raring-backports/multiverse/binary-i386/Packages  404  Not Found [IP: 91.189.91.15 80]
E: Some index files failed to download. They have been ignored, or old ones used instead.
• 0 views • link
updated by Ram Ram • written by weiven90 • weiven90

1 answer

Check your internet connection or how you are connecting to the internet -- your error is stating that you're not able to connect to download or update your dependencies.

Have you tried to update from the command line before? i.e. have you seen this error before?

P.S. Doesn't look like this is a QIIME or bioinformatics issue -- my bet this is a problem with your internet connection or protocol.

• 0 views • link
updated by Ram Ram • written by Josh Herr Josh Herr

Thanks. I now use a local machine with internet but ran into an error described in the updated post

• 0 views • link
written by weiven90 • weiven90

Yes, did you try to:

​sudo pip install numpy
• 0 views • link
updated by Ram Ram • written by Josh Herr Josh Herr

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