Trying to understand python dependencies

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Trying to understand python dependencies

Tony Schreiner
I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.

I was in the process of adding matplotlib from the toolchest. It has a
dependency on package_python_2_7.

Before proceeding, I'd like to understand a bit how that works. Does that
install a whole new python, and how then does it get invoked?

Tony Schreiner

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Re: Trying to understand python dependencies

Gildas Le Corguillé
Hi Tony,

Yes, Galaxy will install a whole functional python version.
At runtime, Galaxy source some env.sh files according to the different requirements and the bunch of requirement dependencies.

Using the tool_dependencies, indeed, Galaxy sets almost a dedicated environment for the tools.

The purpose is the same with the new system Conda. But in this case, Conda can create environment natively

I hope I answered to your question.

Gildas

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Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
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Le 27 juil. 2016 à 17:16, Tony Schreiner <[hidden email]> a écrit :

I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.

I was in the process of adding matplotlib from the toolchest. It has a
dependency on package_python_2_7.

Before proceeding, I'd like to understand a bit how that works. Does that
install a whole new python, and how then does it get invoked?

Tony Schreiner
___________________________________________________________
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Re: Trying to understand python dependencies

Gildas Le Corguillé
I forgot to say that Galaxy installs those dependencies (tool_dependencies or conda) beside your host system.
That will not interfere with your host libraries, binaries ...

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
------------------------------------------------------------------



Le 27 juil. 2016 à 17:41, Gildas Le Corguillé <[hidden email]> a écrit :

Hi Tony,

Yes, Galaxy will install a whole functional python version.
At runtime, Galaxy source some env.sh files according to the different requirements and the bunch of requirement dependencies.

Using the tool_dependencies, indeed, Galaxy sets almost a dedicated environment for the tools.

The purpose is the same with the new system Conda. But in this case, Conda can create environment natively

I hope I answered to your question.

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
------------------------------------------------------------------



Le 27 juil. 2016 à 17:16, Tony Schreiner <[hidden email]> a écrit :

I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.

I was in the process of adding matplotlib from the toolchest. It has a
dependency on package_python_2_7.

Before proceeding, I'd like to understand a bit how that works. Does that
install a whole new python, and how then does it get invoked?

Tony Schreiner
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

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Re: Trying to understand python dependencies

Raymond Wan-2
In reply to this post by Tony Schreiner
Hi Anthony,


On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner
<[hidden email]> wrote:
> I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.
>
> I was in the process of adding matplotlib from the toolchest. It has a
> dependency on package_python_2_7.
>
> Before proceeding, I'd like to understand a bit how that works. Does that
> install a whole new python, and how then does it get invoked?


I have a limited understanding of Galaxy compared to Gildas and many
others here, but it seems that Galaxy and its tools are separated from
the rest of the system.  So, installing a tool won't affect the system
unless your users have set a PATH to Galaxy's tool directory.

For example, when it installs the bwa tool, a bwa executable will get
installed deep within Galaxy's directories.  But as long as your users
set their PATH to /usr/bin or /usr/local/bin or wherever you may have
bwa installed, they'll be fine.  We have this setup where the server
that runs Galaxy also serves users via ssh.  So far, so good --
Galaxy's tool installations don't seem to affect the system's packages
(whether it is something minor like bwa or major like Python).  I'm
afraid I don't know how it is invoked behind-the-scenes, though.

The only issue I've encountered so far is the other way.  Software
installation into the system affects Galaxy.  This was the case with
Samtools and it happened to me just a couple of months ago.  You can
take a look at my question and the many helpful replies I got here:
http://dev.list.galaxyproject.org/Unsorted-BAM-file-gt-Galaxy-crash-td4669457.html
.  It seems to be the case of just samtools for me (so far).

I hoe this helps!

Ray
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Re: Trying to understand python dependencies

Tony Schreiner
Thanks
I'm not worried about it replacing the system python. In general, I am just trying to learn more about how environments are set for jobs.

Tony

On Wed, Jul 27, 2016 at 10:23 PM, Raymond Wan <[hidden email]> wrote:
Hi Anthony,


On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner
<[hidden email]> wrote:
> I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.
>
> I was in the process of adding matplotlib from the toolchest. It has a
> dependency on package_python_2_7.
>
> Before proceeding, I'd like to understand a bit how that works. Does that
> install a whole new python, and how then does it get invoked?


I have a limited understanding of Galaxy compared to Gildas and many
others here, but it seems that Galaxy and its tools are separated from
the rest of the system.  So, installing a tool won't affect the system
unless your users have set a PATH to Galaxy's tool directory.

For example, when it installs the bwa tool, a bwa executable will get
installed deep within Galaxy's directories.  But as long as your users
set their PATH to /usr/bin or /usr/local/bin or wherever you may have
bwa installed, they'll be fine.  We have this setup where the server
that runs Galaxy also serves users via ssh.  So far, so good --
Galaxy's tool installations don't seem to affect the system's packages
(whether it is something minor like bwa or major like Python).  I'm
afraid I don't know how it is invoked behind-the-scenes, though.

The only issue I've encountered so far is the other way.  Software
installation into the system affects Galaxy.  This was the case with
Samtools and it happened to me just a couple of months ago.  You can
take a look at my question and the many helpful replies I got here:
http://dev.list.galaxyproject.org/Unsorted-BAM-file-gt-Galaxy-crash-td4669457.html
.  It seems to be the case of just samtools for me (so far).

I hoe this helps!

Ray


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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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