Help with Installation errors trying to add deeptools to Anaconda

[william...@nih.gov]

Greetings!

 

I am attempting to assist one of our researchers by installing deeptools onto his desktop Windows 7 machine.

 

We have been trying to follow the installation instructions listed athttps://deeptools.readthedocs.io/en/latest/content/installation.html.

 

We have tried to install deeptools from within both the 3.6 and 2.7 versions of Anaconda (both as a standard user and as a local Administrator account). I have run into installation errors in both versions.

 

When I try and use the “conda install” command, I receive a message that deeptools is not available on the default channels.

 

I tried to install using the PIP method, and a pysam dependency could not install. There seems to be some problem with compiling the pysam package.

 

I’ve attached photos of the terminal errors I saw in both error cases.

 

I’ve never used Galaxy, and I had hoped that the Anaconda install method would get this working for my staff member.

 

Any assistance anyone can offer on how I can get the package running would be appreciated!

Best,

Will Jones

Help Desk Technician

National Institute of Arthritis Musculoskeletal and Skin Diseases

NIH

[Björn Grüning]

Hi Will,

Am 07.03.2018 um 15:31 schrieb william...@nih.gov:
> Greetings!
>
> I am attempting to assist one of our researchers by installing deeptools
> onto his desktop Windows 7 machine.
>
> We have been trying to follow the installation instructions listed
> athttps://deeptools.readthedocs.io/en/latest/content/installation.html.
>
> We have tried to install deeptools from within both the 3.6 and 2.7
> versions of Anaconda (both as a standard user and as a local
> Administrator account). I have run into installation errors in both
> versions.
>
> When I try and use the “conda install” command, I receive a message that
> deeptools is not available on the default channels.

Yes, this will not work currently as Bioconda does not build packages
for Windows :(

> I tried to install using the PIP method, and a pysam dependency could
> not install. There seems to be some problem with compiling the pysam
> package.

That very unfortunate.

> I’ve attached photos of the terminal errors I saw in both error cases.

Never seen this before, but I have also not touched a Windows in a decade :(

> I’ve never used Galaxy, and I had hoped that the Anaconda install method
> would get this working for my staff member.

Is your staff member interested in the commandline version of the Galaxy
version?

We do offer Docker containers with deeptools installed for commandline
usage: https://quay.io/repository/biocontainers/deeptools

If you need Galaxy there is also a Galaxy deeptools flavor:
https://quay.io/repository/bgruening/galaxy-deeptools

Or the https://usegalaxy.eu where you can find deeptools installed as well.

> Any assistance anyone can offer on how I can get the package running
> would be appreciated!

Hope anything of this can help,
Sorry for the trouble,
Bjoern

>
> Best,
>
> Will Jones
>
> Help Desk Technician
>
> National Institute of Arthritis Musculoskeletal and Skin Diseases
>
> NIH
>
>
>

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