How to satisfy a Galaxy tool dependency on python-irodsclient

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How to satisfy a Galaxy tool dependency on python-irodsclient

Lawrence, Cris W
I am a Galaxy noob trying to write a Galaxy tool that needs to employ the python-irodsclient module.  I can install it on my laptop via pip.  But I am trying to make it available to Galaxy via planemo.  Apparently, this module is not available in the conda channels.  How else can I satisfy my dependency?  Thanks for any and all help.

- Cris
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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Björn Grüning-3
Hi Chris,

I guess the easiest and recommended way is to use conda.
We can help you to create a conda package for irodclient if you like.

To get you started see here:
https://bioconda.github.io/guidelines.html#python

Cheers,
Bjoern

Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:

> I am a Galaxy noob trying to write a Galaxy tool that needs to employ
> the python-irodsclient module.  I can install it on my laptop via
> pip.  But I am trying to make it available to Galaxy via planemo.
> Apparently, this module is not available in the conda channels.  How
> else can I satisfy my dependency?  Thanks for any and all help.
>
> - Cris ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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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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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Lawrence, Cris W
Bjorn:

Thanks for the tip.  I tried to do a conda build python-irodsclient

BUILD START: python-irodsclient-0.5.0rc1-py27_0

updating index in: //anaconda/conda-bld/osx-64

updating index in: //anaconda/conda-bld/noarch

Can't build /Users/crisl-adm/Tools/python-irodsclient due to unsatisfiable dependencies:

Package missing in current osx-64 channels: 

  - prettytable >=0.7.2


So I tried creating a conda package for prettytable.

It looked to build OK….but I guess I need to upload it to anaconda before I can build python-irodsclient.  I am an anaconda noob as well.  Looks like I need a login.  Where do I acquire a login?

- Cris





On Jan 24, 2017, at 11:17 AM, Björn Grüning <[hidden email]> wrote:

Hi Chris,

I guess the easiest and recommended way is to use conda.
We can help you to create a conda package for irodclient if you like.

To get you started see here:
https://bioconda.github.io/guidelines.html#python

Cheers,
Bjoern

Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
I am a Galaxy noob trying to write a Galaxy tool that needs to employ
the python-irodsclient module.  I can install it on my laptop via
pip.  But I am trying to make it available to Galaxy via planemo.
Apparently, this module is not available in the conda channels.  How
else can I satisfy my dependency?  Thanks for any and all help.

- Cris ___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/



___________________________________________________________
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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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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Björn Grüning-3
Hi Cris,

submit what ever you have to bioconda and we will review and merge it.
It will end up in anaconda.org magically.

If you don't want to use bioconda. You need an anaconda account and then
use `anaconda login`. But be aware that you need to configure Galaxy to
use your package ... bioconda if pre-configured.

Hope that helps,
Bjoern

Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:

> Bjorn:
>
> Thanks for the tip.  I tried to do a conda build python-irodsclient
>
> BUILD START: python-irodsclient-0.5.0rc1-py27_0
>
> updating index in: //anaconda/conda-bld/osx-64
>
> updating index in: //anaconda/conda-bld/noarch
>
> Can't build /Users/crisl-adm/Tools/python-irodsclient due to
> unsatisfiable dependencies:
>
> Package missing in current osx-64 channels:
>
>   - prettytable >=0.7.2
>
>
> So I tried creating a conda package for prettytable.
>
> It looked to build OK….but I guess I need to upload it to anaconda
> before I can build python-irodsclient.  I am an anaconda noob as well.
>  Looks like I need a login.  Where do I acquire a login?
>
> - Cris
>
>
>
>
>
>> On Jan 24, 2017, at 11:17 AM, Björn Grüning <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Hi Chris,
>>
>> I guess the easiest and recommended way is to use conda.
>> We can help you to create a conda package for irodclient if you like.
>>
>> To get you started see here:
>> https://bioconda.github.io/guidelines.html#python
>>
>> Cheers,
>> Bjoern
>>
>> Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
>>> I am a Galaxy noob trying to write a Galaxy tool that needs to employ
>>> the python-irodsclient module.  I can install it on my laptop via
>>> pip.  But I am trying to make it available to Galaxy via planemo.
>>> Apparently, this module is not available in the conda channels.  How
>>> else can I satisfy my dependency?  Thanks for any and all help.
>>>
>>> - Cris ___________________________________________________________
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>>
>
___________________________________________________________
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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  http://galaxyproject.org/search/mailinglists/
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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Lawrence, Cris W
Bjoern:

OK….I am following the recipe submission process, but building in travis-ci is taking longer than I would have expected.  I am over 10 minutes now.  Can you give me some idea of how long a travis-ci build should take?

- Cris

On Jan 24, 2017, at 1:05 PM, Björn Grüning <[hidden email]> wrote:

Hi Cris,

submit what ever you have to bioconda and we will review and merge it.
It will end up in anaconda.org magically.

If you don't want to use bioconda. You need an anaconda account and then
use `anaconda login`. But be aware that you need to configure Galaxy to
use your package ... bioconda if pre-configured.

Hope that helps,
Bjoern

Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:
Bjorn:

Thanks for the tip.  I tried to do a conda build python-irodsclient

BUILD START: python-irodsclient-0.5.0rc1-py27_0

updating index in: //anaconda/conda-bld/osx-64

updating index in: //anaconda/conda-bld/noarch

Can't build /Users/crisl-adm/Tools/python-irodsclient due to
unsatisfiable dependencies:

Package missing in current osx-64 channels: 

 - prettytable >=0.7.2


So I tried creating a conda package for prettytable.

It looked to build OK….but I guess I need to upload it to anaconda
before I can build python-irodsclient.  I am an anaconda noob as well.
Looks like I need a login.  Where do I acquire a login?

- Cris





On Jan 24, 2017, at 11:17 AM, Björn Grüning <[hidden email]
<[hidden email]>> wrote:

Hi Chris,

I guess the easiest and recommended way is to use conda.
We can help you to create a conda package for irodclient if you like.

To get you started see here:
https://bioconda.github.io/guidelines.html#python

Cheers,
Bjoern

Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
I am a Galaxy noob trying to write a Galaxy tool that needs to employ
the python-irodsclient module.  I can install it on my laptop via
pip.  But I am trying to make it available to Galaxy via planemo.
Apparently, this module is not available in the conda channels.  How
else can I satisfy my dependency?  Thanks for any and all help.

- Cris ___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Björn Grüning-3

This depends on how many others are submitting a package. Sorry it takes a while.


On Jan 24, 2017 8:40 PM, "Lawrence, Cris W" <[hidden email]> wrote:
Bjoern:

OK….I am following the recipe submission process, but building in travis-ci is taking longer than I would have expected.  I am over 10 minutes now.  Can you give me some idea of how long a travis-ci build should take?

- Cris

On Jan 24, 2017, at 1:05 PM, Björn Grüning <[hidden email]> wrote:

Hi Cris,

submit what ever you have to bioconda and we will review and merge it.
It will end up in anaconda.org magically.

If you don't want to use bioconda. You need an anaconda account and then
use `anaconda login`. But be aware that you need to configure Galaxy to
use your package ... bioconda if pre-configured.

Hope that helps,
Bjoern

Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:
Bjorn:

Thanks for the tip.  I tried to do a conda build python-irodsclient

BUILD START: python-irodsclient-0.5.0rc1-py27_0

updating index in: //anaconda/conda-bld/osx-64

updating index in: //anaconda/conda-bld/noarch

Can't build /Users/crisl-adm/Tools/python-irodsclient due to
unsatisfiable dependencies:

Package missing in current osx-64 channels: 

 - prettytable >=0.7.2


So I tried creating a conda package for prettytable.

It looked to build OK….but I guess I need to upload it to anaconda
before I can build python-irodsclient.  I am an anaconda noob as well.
Looks like I need a login.  Where do I acquire a login?

- Cris





On Jan 24, 2017, at 11:17 AM, Björn Grüning <[hidden email]
<[hidden email]>> wrote:

Hi Chris,

I guess the easiest and recommended way is to use conda.
We can help you to create a conda package for irodclient if you like.

To get you started see here:
https://bioconda.github.io/guidelines.html#python

Cheers,
Bjoern

Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
I am a Galaxy noob trying to write a Galaxy tool that needs to employ
the python-irodsclient module.  I can install it on my laptop via
pip.  But I am trying to make it available to Galaxy via planemo.
Apparently, this module is not available in the conda channels.  How
else can I satisfy my dependency?  Thanks for any and all help.

- Cris ___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Lawrence, Cris W
Bjoern

Sorry to be a pest.  One other question before I attempt any PR.  The python-irodsclient is not itself a bioinformatics tool - it’s a wrapper for communicating with iRODS - a data management system and its dependency, pretty tables, I would surmise, is just a utility.  After reading the bioconda policy, I am wondering whether these items belong in the bioconda channel.  If not, is there a more appropriate channel?

- Cris

On Jan 24, 2017, at 3:09 PM, [hidden email] <[hidden email]> wrote:

This depends on how many others are submitting a package. Sorry it takes a while.


On Jan 24, 2017 8:40 PM, "Lawrence, Cris W" <[hidden email]> wrote:
Bjoern:

OK….I am following the recipe submission process, but building in travis-ci is taking longer than I would have expected.  I am over 10 minutes now.  Can you give me some idea of how long a travis-ci build should take?

- Cris

On Jan 24, 2017, at 1:05 PM, Björn Grüning <[hidden email]> wrote:

Hi Cris,

submit what ever you have to bioconda and we will review and merge it.
It will end up in anaconda.org magically.

If you don't want to use bioconda. You need an anaconda account and then
use `anaconda login`. But be aware that you need to configure Galaxy to
use your package ... bioconda if pre-configured.

Hope that helps,
Bjoern

Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:
Bjorn:

Thanks for the tip.  I tried to do a conda build python-irodsclient

BUILD START: python-irodsclient-0.5.0rc1-py27_0

updating index in: //anaconda/conda-bld/osx-64

updating index in: //anaconda/conda-bld/noarch

Can't build /Users/crisl-adm/Tools/python-irodsclient due to
unsatisfiable dependencies:

Package missing in current osx-64 channels: 

 - prettytable >=0.7.2


So I tried creating a conda package for prettytable.

It looked to build OK….but I guess I need to upload it to anaconda
before I can build python-irodsclient.  I am an anaconda noob as well.
Looks like I need a login.  Where do I acquire a login?

- Cris





On Jan 24, 2017, at 11:17 AM, Björn Grüning <[hidden email]
<[hidden email]>> wrote:

Hi Chris,

I guess the easiest and recommended way is to use conda.
We can help you to create a conda package for irodclient if you like.

To get you started see here:
https://bioconda.github.io/guidelines.html#python

Cheers,
Bjoern

Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
I am a Galaxy noob trying to write a Galaxy tool that needs to employ
the python-irodsclient module.  I can install it on my laptop via
pip.  But I am trying to make it available to Galaxy via planemo.
Apparently, this module is not available in the conda channels.  How
else can I satisfy my dependency?  Thanks for any and all help.

- Cris ___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/



___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: How to satisfy a Galaxy tool dependency on python-irodsclient

Björn Grüning-3
Hi Cris,

yes there is a better channel - it is conda-forge. But it will take you
even more time to submit there and a more strict review.

I would encourage you to submit to conda-forge, but for a starter and to
not discourage you for the first time experience I recommended bioconda
-- here I can assist you more.

It up to you, I will try my best to guide you,
Bjoern

Am 24.01.2017 um 21:27 schrieb Lawrence, Cris W:

> Bjoern
>
> Sorry to be a pest.  One other question before I attempt any PR.  The
> python-irodsclient is not itself a bioinformatics tool - it’s a wrapper
> for communicating with iRODS - a data management system and its
> dependency, pretty tables, I would surmise, is just a utility.  After
> reading the bioconda policy, I am wondering whether these items belong
> in the bioconda channel.  If not, is there a more appropriate channel?
>
> - Cris
>
>> On Jan 24, 2017, at 3:09 PM, [hidden email]
>> <mailto:[hidden email]> <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> This depends on how many others are submitting a package. Sorry it
>> takes a while.
>>
>>
>> On Jan 24, 2017 8:40 PM, "Lawrence, Cris W" <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Bjoern:
>>
>>     OK….I am following the recipe submission process, but building in
>>     travis-ci is taking longer than I would have expected.  I am over
>>     10 minutes now.  Can you give me some idea of how long a travis-ci
>>     build should take?
>>
>>     - Cris
>>
>>>     On Jan 24, 2017, at 1:05 PM, Björn Grüning
>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>
>>>     Hi Cris,
>>>
>>>     submit what ever you have to bioconda and we will review and
>>>     merge it.
>>>     It will end up in anaconda.org <http://anaconda.org/> magically.
>>>
>>>     If you don't want to use bioconda. You need an anaconda account
>>>     and then
>>>     use `anaconda login`. But be aware that you need to configure
>>>     Galaxy to
>>>     use your package ... bioconda if pre-configured.
>>>
>>>     Hope that helps,
>>>     Bjoern
>>>
>>>     Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:
>>>>     Bjorn:
>>>>
>>>>     Thanks for the tip.  I tried to do a conda build python-irodsclient
>>>>
>>>>     BUILD START: python-irodsclient-0.5.0rc1-py27_0
>>>>
>>>>     updating index in: //anaconda/conda-bld/osx-64
>>>>
>>>>     updating index in: //anaconda/conda-bld/noarch
>>>>
>>>>     Can't build /Users/crisl-adm/Tools/python-irodsclient due to
>>>>     unsatisfiable dependencies:
>>>>
>>>>     Package missing in current osx-64 channels:
>>>>
>>>>      - prettytable >=0.7.2
>>>>
>>>>
>>>>     So I tried creating a conda package for prettytable.
>>>>
>>>>     It looked to build OK….but I guess I need to upload it to anaconda
>>>>     before I can build python-irodsclient.  I am an anaconda noob as
>>>>     well.
>>>>     Looks like I need a login.  Where do I acquire a login?
>>>>
>>>>     - Cris
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>     On Jan 24, 2017, at 11:17 AM, Björn Grüning
>>>>>     <[hidden email] <mailto:[hidden email]>
>>>>>     <mailto:[hidden email]
>>>>>     <mailto:[hidden email]>>> wrote:
>>>>>
>>>>>     Hi Chris,
>>>>>
>>>>>     I guess the easiest and recommended way is to use conda.
>>>>>     We can help you to create a conda package for irodclient if you
>>>>>     like.
>>>>>
>>>>>     To get you started see here:
>>>>>     https://bioconda.github.io/guidelines.html#python
>>>>>     <https://bioconda.github.io/guidelines.html#python>
>>>>>
>>>>>     Cheers,
>>>>>     Bjoern
>>>>>
>>>>>     Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
>>>>>>     I am a Galaxy noob trying to write a Galaxy tool that needs to
>>>>>>     employ
>>>>>>     the python-irodsclient module.  I can install it on my laptop via
>>>>>>     pip.  But I am trying to make it available to Galaxy via planemo.
>>>>>>     Apparently, this module is not available in the conda
>>>>>>     channels.  How
>>>>>>     else can I satisfy my dependency?  Thanks for any and all help.
>>>>>>
>>>>>>     - Cris ___________________________________________________________
>>>>>>     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/
>>>>>>     <https://lists.galaxyproject.org/>
>>>>>>
>>>>>>     To search Galaxy mailing lists use the unified search at:
>>>>>>     http://galaxyproject.org/search/mailinglists/
>>>>>>     <http://galaxyproject.org/search/mailinglists/>
>>
>
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/