PySam installation using Wheels

[Karel Břinda]

Hello,

installation of PySam takes really much time and it is a problem especially for continuous integration servers (e.g., Travis CI which is now very popular in combination with GitHub). It should be technically simple to create wheel files of PySam to make its installation faster (http://pythonwheels.com/).

See this thread: https://github.com/ga4gh/server/issues/71

They are building this PySam package: http://www.well.ox.ac.uk/~jk/wheelhouse.tar.

It would be very nice if there existed an official wheel file for PySam which people could use in their projects. For example, I cannot use the Oxford one since they create it only for Python 2.7.

Best

Karel Brinda

[Sebastian Luna Valero]

Hello Karel,

In case it is of interest, we build Conda packages for Pysam:
https://conda.binstar.org/cgat

You just need to install conda and use CGAT's binstar channel:
conda install -c https://conda.binstar.org/cgat pysam

to get it installed very quickly.

Best regards,

Sebastian.

PS: More information about Conda can be found here http://conda.pydata.org/docs/

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[Karel Břinda]

Hi Sebastian,

thank you for your answer. I use (Ana)Conda on my laptops and desktops and I like it. However, the problem with PySam is that a Conda package exists only for Python 2.7.

Currently I develop almost all my programs in SnakeMake (Python-based Make-like environment for bioinformatics, https://bitbucket.org/johanneskoester/snakemake/wiki/Home) which requires at least Python 3.2. On Travis I usually write tests for Python 3.2, 3.3 and 3.4.

Best regards

Karel

[Andreas Heger]

Hi Karel,

building wheels is on top our todo list. Kevin has already started work
on this, but I think python 3 still needs doing. I will get back to you.

Best wishes,
Andreas

On 03/17/15 13:06, Karel Břinda wrote:
> Hi Sebastian,
>
> thank you for your answer. I use (Ana)Conda on my laptops and desktops
> and I like it. However, the problem with PySam is that a Conda package
> exists only for Python 2.7.
>
> Currently I develop almost all my programs in SnakeMake (Python-based
> Make-like environment for bioinformatics,
> https://bitbucket.org/johanneskoester/snakemake/wiki/Home) which
> requires at least Python 3.2. On Travis I usually write tests for Python
> 3.2, 3.3 and 3.4.
>
> Best regards
>
> Karel
>
>
>
> 2015-03-17 13:25 GMT+01:00 Sebastian Luna Valero

> <sebastian....@gmail.com <mailto:sebastian....@gmail.com>>:

>
>
> Hello Karel,
>
> In case it is of interest, we build Conda packages for Pysam:
> https://conda.binstar.org/cgat
>
> You just need to install conda and use CGAT's binstar channel:
> conda install -c https://conda.binstar.org/cgat pysam
>
> to get it installed very quickly.
>
> Best regards,
> Sebastian.
>
> PS: More information about Conda can be found here
> http://conda.pydata.org/docs/
>
>
> 2015-03-17 11:58 GMT+00:00 Karel Břinda <karel....@gmail.com

> <mailto:karel....@gmail.com>>:

>
> Hello,
>
> installation of PySam takes really much time and it is a problem
> especially for continuous integration servers (e.g., Travis CI
> which is now very popular in combination with GitHub). It should
> be technically simple to create wheel files of PySam to make its
> installation faster (http://pythonwheels.com/).
>
> See this thread: https://github.com/ga4gh/server/issues/71
> They are building this PySam package:
> http://www.well.ox.ac.uk/~jk/wheelhouse.tar.
>
> It would be very nice if there existed an official wheel file
> for PySam which people could use in their projects. For example,
> I cannot use the Oxford one since they create it only for Python
> 2.7.
>
> Best
>
> Karel Brinda
>
> --
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> To unsubscribe from this group and stop receiving emails from
> it, send an email to
> pysam-user-gro...@googlegroups.com

> <mailto:pysam-user-gro...@googlegroups.com>.

> For more options, visit https://groups.google.com/d/optout.
>
>
> --
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>
> For more options, visit https://groups.google.com/d/optout.
>
>
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[Andreas]

Hi Karel,

I have put wheels at:

https://www.cgat.org/downloads/public/pysam/wheels/

Please let me know if they work for you. I will aim to keep this updated for new pysam releases.

Best wishes,
Andreas

[Karel Břinda]

Hi Andreas,

I tested it and it works well. Great! Thank you.

I believe that it can be automated -- I think that the wheels can be created by Travis (and you can choose if only for commits/merges to branch master or only for tagged commits). Also other versions of Python could be easily supported. Currently, there are wheels for Python 2.7 and Python 3.4. With Travis, you could make wheels also for Python 3.2, 3.2, and 3.5 (nightly builds).

If anyone else wants to use it on Travis, my corresponding lines in .travis.yml are:

before_install:
- wget -A *.whl -nd -r --no-parent http://www.cgat.org/downloads/public/pysam/wheels/
install:
- pip install --use-wheel --find-links=./ -r requirements.txt

Best regards

Karel

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[Andreas Heger]

Hi Karel,

great, and tanks for the tip, that is a useful. I will look into this.

Best wishes,
Andreas

On 03/26/15 22:33, Karel Břinda wrote:
> Hi Andreas,
>
> I tested it and it works well. Great! Thank you.
>
> I believe that it can be automated -- I think that the wheels can be
> created by Travis (and you can choose if only for commits/merges to
> branch master or only for tagged commits). Also other versions of Python
> could be easily supported. Currently, there are wheels for Python 2.7
> and Python 3.4. With Travis, you could make wheels also for Python 3.2,
> 3.2, and 3.5 (nightly builds).
>
> If anyone else wants to use it on Travis, my corresponding lines in
> .travis.yml are:
>
> before_install:
> - wget -A *.whl -nd -r --no-parent
> http://www.cgat.org/downloads/public/pysam/wheels/
> install:
> - pip install --use-wheel --find-links=./ -r requirements.txt
>
> Best regards
>
> Karel
>
>
>
> 2015-03-26 21:16 GMT+01:00 Andreas <andrea...@gmail.com

> <mailto:andrea...@gmail.com>>:

>
> Hi Karel,
>
> I have put wheels at:
>
> https://www.cgat.org/downloads/public/pysam/wheels/
>
> Please let me know if they work for you. I will aim to keep this
> updated for new pysam releases.
>
> Best wishes,
> Andreas
>
>
>
> --
> You received this message because you are subscribed to the Google
> Groups "Pysam User group" group.
> To unsubscribe from this group and stop receiving emails from it,
> send an email to pysam-user-gro...@googlegroups.com

> <mailto:pysam-user-gro...@googlegroups.com>.

>
> For more options, visit https://groups.google.com/d/optout.
>
>

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