Question regarding anaconda installation of deepTools

[Blais Lab]

Hello

We'd like to install deepTools locally (Ubuntu Linux), and we're having a problem.

The following command:

$ conda install -c bioconda deeptools

works fine until this step:

Fetching packages ...
curl-7.45.0-1. 100% |################################################################################################| Time: 0:00:00   4.22 MB/s
libxml2-2.9.3- 100% |################################################################################################| Time: 0:00:00  14.76 MB/s
Could not connect to https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.2.5-py27_0.tar.bz2
Error: Connection error: EOF occurred in violation of protocol (_ssl.c:590): https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.2.5-py27_0.tar.bz2

I can actually download the bz2 file just fine, using Firefox on the same workstation, and it extracts fine (although I don't have MD5 values to check) so I don't think it is a problem with availability or integrity of the file.

I am not familiar with ssl protocol violation... I am wondering if you can offer some help.

Thanks in advance.

Alex

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Alexandre Blais, Ph.D. Principal Investigator

Ottawa Institute of Systems Biology
BMI Department - University of Ottawa
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Blais.la...@gmail.com

[Devon Ryan]

Hi Alex,

Presumably there was a transient network or server error somewhere. Either try again or just download the file in firefox and "conda install pybigwig-0.2.5-px27_0.tar.bz2" (assuming you're in the same directory as the file).

Devon

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Devon Ryan, PhD
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Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dpry...@gmail.com

[blais.la...@gmail.com]

Hi Devon
Thanks for your reply. I managed to install the pybigwig package manually, as you instructed.
I think you are right about it being a network or server issue. Now additional packages (deeptools itself) take forever to be fetched... I suppose I just need to be patient.

Is there a command to issue to test if the installation worked properly?
I am looking for a basic tutorial for the command-line, but most of the (excellent) documentation relates to the Galaxy implementation.

Thanks again.
Alex

[Friederike Dündar]

Hi Alex,

to check whether the installation of deepTools succeeded, you can simply type the name of any tool and call the help, e.g.:

plotPCA --help

You should then see the details of the tool's parameters.

The documentation also contains usage examples for the individual tools focusing on command line commands: http://deeptools.readthedocs.org/en/latest/content/list_of_tools.html

However, all of the options available in Galaxy are also available on the command line.

Hope that helps.

Best,

Friederike

[Devon Ryan]

Hi Alex,

You can run our automated tests with "nosetests --with-doctest
--ignore-files=plotCoverage deeptools". That'll run ~68 tests and
ensure most of the tools are working properly. If that passes then you
can trust that everything was installed successfully.

Devon
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Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany