How can I install qiime1 by using the miniconda successfully?

[dxccat]

I try to install qiime1 on my Linux system Ubuntu 16.04 by following the miniconda protocal. When downloading the file libxml2-2.9.3-0.tar.bz2, the network speed is low and always blocked. The error is like below:

Fetching packages ...

An unexpected error has occurred.############                                                                                                                                    | ETA:  0:16:51   4.56 kB/s

Please consider posting the following information to the

conda GitHub issue tracker at:

    https://github.com/conda/conda/issues

Current conda install:

               platform : linux-64

          conda version : 4.2.12

       conda is private : False

      conda-env version : 4.2.12

    conda-build version : not installed

         python version : 3.5.2.final.0

       requests version : 2.11.1

       root environment : /home/dxccat/miniconda3  (writable)

    default environment : /home/dxccat/miniconda3

       envs directories : /home/dxccat/miniconda3/envs

          package cache : /home/dxccat/miniconda3/pkgs

           channel URLs : https://repo.continuum.io/pkgs/free/linux-64

                          https://repo.continuum.io/pkgs/free/noarch

                          https://repo.continuum.io/pkgs/pro/linux-64

                          https://repo.continuum.io/pkgs/pro/noarch

            config file : None

           offline mode : False

`$ /home/dxccat/miniconda3/bin/conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda`

    Traceback (most recent call last):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/packages/urllib3/response.py", line 232, in _error_catcher

        yield

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/packages/urllib3/response.py", line 314, in read

        data = self._fp.read(amt)

      File "/home/dxccat/miniconda3/lib/python3.5/http/client.py", line 448, in read

        n = self.readinto(b)

      File "/home/dxccat/miniconda3/lib/python3.5/http/client.py", line 488, in readinto

        n = self.fp.readinto(b)

      File "/home/dxccat/miniconda3/lib/python3.5/socket.py", line 575, in readinto

        return self._sock.recv_into(b)

      File "/home/dxccat/miniconda3/lib/python3.5/ssl.py", line 929, in recv_into

        return self.read(nbytes, buffer)

      File "/home/dxccat/miniconda3/lib/python3.5/ssl.py", line 791, in read

        return self._sslobj.read(len, buffer)

      File "/home/dxccat/miniconda3/lib/python3.5/ssl.py", line 575, in read

        v = self._sslobj.read(len, buffer)

    socket.timeout: The read operation timed out

    

    During handling of the above exception, another exception occurred:

    

    Traceback (most recent call last):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/models.py", line 676, in generate

        for chunk in self.raw.stream(chunk_size, decode_content=True):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/packages/urllib3/response.py", line 357, in stream

        data = self.read(amt=amt, decode_content=decode_content)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/packages/urllib3/response.py", line 324, in read

        flush_decoder = True

      File "/home/dxccat/miniconda3/lib/python3.5/contextlib.py", line 77, in __exit__

        self.gen.throw(type, value, traceback)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/packages/urllib3/response.py", line 237, in _error_catcher

        raise ReadTimeoutError(self._pool, None, 'Read timed out.')

    requests.packages.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='binstar-cio-packages-prod.s3.amazonaws.com', port=443): Read timed out.

    

    During handling of the above exception, another exception occurred:

    

    Traceback (most recent call last):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/fetch.py", line 431, in download

        for chunk in resp.iter_content(2**14):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/requests/models.py", line 683, in generate

        raise ConnectionError(e)

    requests.exceptions.ConnectionError: HTTPSConnectionPool(host='binstar-cio-packages-prod.s3.amazonaws.com', port=443): Read timed out.

    

    During handling of the above exception, another exception occurred:

    

    Traceback (most recent call last):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/cli/install.py", line 405, in install

        execute_actions(actions, index, verbose=not context.quiet)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/plan.py", line 643, in execute_actions

        inst.execute_instructions(plan, index, verbose)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/instructions.py", line 134, in execute_instructions

        cmd(state, arg)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/instructions.py", line 47, in FETCH_CMD

        fetch_pkg(state['index'][arg + '.tar.bz2'])

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/fetch.py", line 363, in fetch_pkg

        download(url, path, session=session, md5=info['md5'], urlstxt=True)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/fetch.py", line 450, in download

        raise CondaRuntimeError("Could not open %r for writing (%s)." % (pp, e))

    conda.exceptions.CondaRuntimeError: Runtime error: Could not open '/home/dxccat/miniconda3/pkgs/libxml2-2.9.3-0.tar.bz2.part' for writing (HTTPSConnectionPool(host='binstar-cio-packages-prod.s3.amazonaws.com', port=443): Read timed out.).

    

    During handling of the above exception, another exception occurred:

    

    Traceback (most recent call last):

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/exceptions.py", line 479, in conda_exception_handler

        return_value = func(*args, **kwargs)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/cli/main.py", line 145, in _main

        exit_code = args.func(args, p)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/cli/main_create.py", line 68, in execute

        install(args, parser, 'create')

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/cli/install.py", line 422, in install

        raise CondaSystemExit('Exiting', e)

      File "/home/dxccat/miniconda3/lib/python3.5/contextlib.py", line 77, in __exit__

        self.gen.throw(type, value, traceback)

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/cli/common.py", line 573, in json_progress_bars

        yield

      File "/home/dxccat/miniconda3/lib/python3.5/site-packages/conda/cli/install.py", line 420, in install

        raise CondaRuntimeError('RuntimeError: %s' % e)

    conda.exceptions.CondaRuntimeError: Runtime error: RuntimeError: Runtime error: Could not open '/home/dxccat/miniconda3/pkgs/libxml2-2.9.3-0.tar.bz2.part' for writing (HTTPSConnectionPool(host='binstar-cio-packages-prod.s3.amazonaws.com', port=443): Read timed out.).

    I know this maybe the reason of the state firewall policy of mainland China, so I tried to change the hosts file and use some proxy, but failed...

    And I tried to download the file libxml2-2.9.3-0.tar.bz2 manually through the browser successfully and put the file into the folder /home/dxccat/miniconda3/pkgs, but how can I let minicoda know this file has already exist and ignore downloading this file again? This maybe the only way I can install qiime1 successfully.

    Please help me to solve the issue, thanks a lot!

[jonsan]

That's a tricky one!

Here's some code I've used to manually install a C library into a conda environment:

# GSL

export C_INCLUDE_PATH=$C_INCLUDE_PATH:${condaenv}/include/

export LIBRARY_PATH=$LIBRARY_PATH:${condaenv}/lib

cd ${condaenv}

wget ftp://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz

tar -xzvf gsl-latest.tar.gz

cd gsl-2.1/

./configure --prefix=${condaenv}

make

make install

Does that help?

[dxccat]

Hi, Jonsan

Based on my miniconda environment, I changed ${condaenv} to miniconda3/ and installed this C library successfully.

But, is that correct? I'm new on linux command and I don't know whether changing ${condaenv} to miniconda3 is right or not.

After that, I tried to re-install qiime1 several times and found some packages are still hard to download for the low connection speed. Maybe I need to switch to another internet environment or do something else?

[jonsan]

Hi, 

Sorry for not being a bit more clear in that example; $condaenv should be set not to the miniconda3 folder but to the specific environment in which you want to install the library. (for example ~/miniconda3/envs/qiime). It's a little bit of a hack so you might want to find someone local who's relatively familiar with Linux who can maybe look over your shoulder in case anything comes up. 

Another option would be to install via the Qiime virtual box, which should contain everything you need in one place.

-jon