How to satisfy a Galaxy tool dependency on python-irodsclient
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
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/
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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 <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>> 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/
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 <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> 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/
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 <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>> 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 <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com> <mailto:bjoern.gruening@gmail.com>> 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/
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" <crisl@upenn.edu> 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 <bjoern.gruening@gmail.com> 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 <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com <bjoern.gruening@gmail.com>>> 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/
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, bjoern.gruening@googlemail.com<mailto:bjoern.gruening@googlemail.com> <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>> 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" <crisl@upenn.edu<mailto:crisl@upenn.edu>> 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 <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>> 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 <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com> <mailto:bjoern.gruening@gmail.com>> 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/
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, bjoern.gruening@googlemail.com <mailto:bjoern.gruening@googlemail.com> <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> 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" <crisl@upenn.edu <mailto:crisl@upenn.edu>> 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 <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> 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 <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com> <mailto:bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>>> 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/>
participants (3)
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bjoern.gruening＠googlemail.com -
Björn Grüning
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Lawrence, Cris W