I wrote the tool because when I ran planemo it found the tool_depencecy file but then logged that it could not find the actual tools. So 1. Did you install the dependecies into the galaxy you are using to run planemo? If not my tool will not work until you do. 2. When you run the test does the log show it looked for but could not find python_nltk_tools? If not then the error is outside of the scope of the tool. Christian ________________________________ From: Steve Cassidy [steve.cassidy@mq.edu.au] Sent: Friday, September 04, 2015 11:41 AM To: Christian Brenninkmeijer Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo and tool dependencies Thanks Christian, I'm not sure I understand how to make use of this. My tool dependency is described in an XML file which is in the same source directory as the tool xml and python files. The tool xml file contains: <requirement type="package" version="1.0">python_nltk_tools</requirement> and the tool_dependencies.xml file contains the definition: <tool_dependency> <package name="python_nltk_tools" version="1.0"> ... how do I tell planemo to tell galaxy that it should refer to this tool dependency file to resolve the requirement? At the moment it's loading all of the tools but doesn't seem to be concerned that the requirement isn't met. Thanks for your help. Steve On 3 September 2015 at 18:06, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk<mailto:christian.brenninkmeijer@manchester.ac.uk>> wrote: Hi, I wrote an extension that will help planemo pull in tool dependencies. See https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/re... It is for when the dependency was installed into galaxy but where planemo is not using the database to find that tool. It works my helping planemo guess where the tool dependency may be. Hope that helps. Christian University of Manchester ________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org<mailto:galaxy-dev-bounces@lists.galaxyproject.org>] on behalf of Steve Cassidy [steve.cassidy@mq.edu.au<mailto:steve.cassidy@mq.edu.au>] Sent: Thursday, September 03, 2015 9:00 AM To: galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Subject: [galaxy-dev] planemo and tool dependencies Hi all, I'm trying to test some tools under planemo and can't find out how to have it install tool dependencies while setting up the environment. The dependency is on a particular python module and we have a tool_dependencies.xml file to describe it. I can't see a way to tell planemo serve etc to refer to that file to get the dependencies. Any help appreciated. Steve -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/ -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

Hi Steve, You would need to create a too_depencency and load it to a tool shed. Then install it from that tool shed to your galaxy. Unless someone who know galaxy better jumps and says there is another way! Christian PS. Either uses the testtoolshed or start your own. ________________________________ From: Steve Cassidy [steve.cassidy@mq.edu.au] Sent: Friday, September 04, 2015 12:29 PM To: Christian Brenninkmeijer Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo and tool dependencies On 4 September 2015 at 21:00, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk<mailto:christian.brenninkmeijer@manchester.ac.uk>> wrote: I wrote the tool because when I ran planemo it found the tool_depencecy file but then logged that it could not find the actual tools. So 1. Did you install the dependecies into the galaxy you are using to run planemo? If not my tool will not work until you do. I didn't do this - how do I do this? Do I install the modules into the --tool_dependency_dir ? 2. When you run the test does the log show it looked for but could not find python_nltk_tools? If not then the error is outside of the scope of the tool. Yes, it said: galaxy.tools.deps DEBUG 2015-09-04 20:55:32,054 Building dependency shell command for dependency 'python_nltk_tools' galaxy.tools.deps.resolvers.unlinked_tool_shed_packages DEBUG 2015-09-04 20:55:32,054 Unable to find dependency,'python_nltk_tools' '1.0' 'package' galaxy.tools.deps WARNING 2015-09-04 20:55:32,054 Failed to resolve dependency on 'python_nltk_tools', ignoring Thanks, Steve Christian ________________________________ From: Steve Cassidy [steve.cassidy@mq.edu.au<mailto:steve.cassidy@mq.edu.au>] Sent: Friday, September 04, 2015 11:41 AM To: Christian Brenninkmeijer Cc: galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] planemo and tool dependencies Thanks Christian, I'm not sure I understand how to make use of this. My tool dependency is described in an XML file which is in the same source directory as the tool xml and python files. The tool xml file contains: <requirement type="package" version="1.0">python_nltk_tools</requirement> and the tool_dependencies.xml file contains the definition: <tool_dependency> <package name="python_nltk_tools" version="1.0"> ... how do I tell planemo to tell galaxy that it should refer to this tool dependency file to resolve the requirement? At the moment it's loading all of the tools but doesn't seem to be concerned that the requirement isn't met. Thanks for your help. Steve On 3 September 2015 at 18:06, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk<mailto:christian.brenninkmeijer@manchester.ac.uk>> wrote: Hi, I wrote an extension that will help planemo pull in tool dependencies. See https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/re... It is for when the dependency was installed into galaxy but where planemo is not using the database to find that tool. It works my helping planemo guess where the tool dependency may be. Hope that helps. Christian University of Manchester ________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org<mailto:galaxy-dev-bounces@lists.galaxyproject.org>] on behalf of Steve Cassidy [steve.cassidy@mq.edu.au<mailto:steve.cassidy@mq.edu.au>] Sent: Thursday, September 03, 2015 9:00 AM To: galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Subject: [galaxy-dev] planemo and tool dependencies Hi all, I'm trying to test some tools under planemo and can't find out how to have it install tool dependencies while setting up the environment. The dependency is on a particular python module and we have a tool_dependencies.xml file to describe it. I can't see a way to tell planemo serve etc to refer to that file to get the dependencies. Any help appreciated. Steve -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/ -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/ -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

Hello Steve, It seems you figured it out so just to summarize: Planemo does not have a good built-in way to install tool dependencies yet. We are considering using Homebrew ( http://planemo.readthedocs.org/en/latest/readme.html#brew) but until that is implemented Planemo will just use whatever it can see on the system. The script from Christian looks very nice, I have to try it. :) Thank you for using Planemo Martin On Fri, Sep 4, 2015 at 8:21 AM Steve Cassidy <steve.cassidy@mq.edu.au> wrote:

Ok, thanks, I'll try to work that out. Meanwhile I've got my tools working in planemo test mode - it now seems to be using the installed python libraries where earlier it was creating a fresh venv - I updated my galaxy sources.

Thanks for your help.

Steve

On 4 September 2015 at 22:09, Christian Brenninkmeijer < christian.brenninkmeijer@manchester.ac.uk> wrote:

...

Hi Steve, You would need to create a too_depencency and load it to a tool shed.

Then install it from that tool shed to your galaxy.

Unless someone who know galaxy better jumps and says there is another way!

Christian

PS. Either uses the testtoolshed or start your own.

------------------------------ *From:* Steve Cassidy [steve.cassidy@mq.edu.au] *Sent:* Friday, September 04, 2015 12:29 PM

*To:* Christian Brenninkmeijer *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] planemo and tool dependencies

On 4 September 2015 at 21:00, Christian Brenninkmeijer < christian.brenninkmeijer@manchester.ac.uk> wrote:

...

I wrote the tool because when I ran planemo it found the tool_depencecy file but then logged that it could not find the actual tools.

So 1. Did you install the dependecies into the galaxy you are using to run planemo? If not my tool will not work until you do.

I didn't do this - how do I do this? Do I install the modules into the --tool_dependency_dir ?

...

2. When you run the test does the log show it looked for but could not find python_nltk_tools? If not then the error is outside of the scope of the tool.

Yes, it said:

galaxy.tools.deps DEBUG 2015-09-04 20:55:32,054 Building dependency shell command for dependency 'python_nltk_tools' galaxy.tools.deps.resolvers.unlinked_tool_shed_packages DEBUG 2015-09-04 20:55:32,054 Unable to find dependency,'python_nltk_tools' '1.0' 'package' galaxy.tools.deps WARNING 2015-09-04 20:55:32,054 Failed to resolve dependency on 'python_nltk_tools', ignoring

Thanks,

Steve

...

Christian ------------------------------ *From:* Steve Cassidy [steve.cassidy@mq.edu.au] *Sent:* Friday, September 04, 2015 11:41 AM *To:* Christian Brenninkmeijer *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] planemo and tool dependencies

Thanks Christian, I'm not sure I understand how to make use of this. My tool dependency is described in an XML file which is in the same source directory as the tool xml and python files. The tool xml file contains:

<requirement type="package" version="1.0">python_nltk_tools</requirement>

and the tool_dependencies.xml file contains the definition:

<tool_dependency> <package name="python_nltk_tools" version="1.0"> ...

how do I tell planemo to tell galaxy that it should refer to this tool dependency file to resolve the requirement? At the moment it's loading all of the tools but doesn't seem to be concerned that the requirement isn't met.

Thanks for your help.

Steve

On 3 September 2015 at 18:06, Christian Brenninkmeijer < christian.brenninkmeijer@manchester.ac.uk> wrote:

...

Hi,

I wrote an extension that will help planemo pull in tool dependencies.

See https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/re...

It is for when the dependency was installed into galaxy but where planemo is not using the database to find that tool.

It works my helping planemo guess where the tool dependency may be.

Hope that helps. Christian University of Manchester ------------------------------ *From:* galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Steve Cassidy [steve.cassidy@mq.edu.au] *Sent:* Thursday, September 03, 2015 9:00 AM *To:* galaxy-dev@lists.galaxyproject.org *Subject:* [galaxy-dev] planemo and tool dependencies

Hi all, I'm trying to test some tools under planemo and can't find out how to have it install tool dependencies while setting up the environment.

The dependency is on a particular python module and we have a tool_dependencies.xml file to describe it. I can't see a way to tell planemo serve etc to refer to that file to get the dependencies.

Any help appreciated.

Steve

-- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

-- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

-- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

-- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/ ___________________________________________________________ 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 All, A perfect but much harder solution would be for planemo to keep its own dependency database. Which when testing tools would be checked, updated if required and then used. But that is completely beyond anything I am interested in doing. Christian ________________________________________ From: John Chilton [jmchilton@gmail.com] Sent: Wednesday, September 09, 2015 4:56 PM To: Christian Brenninkmeijer Cc: Steve Cassidy; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo and tool dependencies Thanks again for implementing this Christian and for outlining how to maybe use it for testing. I'll try to add some support and documentation to planemo for how to use it - https://github.com/galaxyproject/planemo/issues/290 - it is not my favorite long term 100% solution to this problem - but it is a fantastic 95% solution that I think people could get a lot of traction out of if we added some support to planemo and documented how to test using it. -John On Fri, Sep 4, 2015 at 12:00 PM, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk> wrote:

I wrote the tool because when I ran planemo it found the tool_depencecy file but then logged that it could not find the actual tools.

So 1. Did you install the dependecies into the galaxy you are using to run planemo? If not my tool will not work until you do.

2. When you run the test does the log show it looked for but could not find python_nltk_tools? If not then the error is outside of the scope of the tool.

Christian ________________________________ From: Steve Cassidy [steve.cassidy@mq.edu.au] Sent: Friday, September 04, 2015 11:41 AM To: Christian Brenninkmeijer Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo and tool dependencies

Thanks Christian, I'm not sure I understand how to make use of this. My tool dependency is described in an XML file which is in the same source directory as the tool xml and python files. The tool xml file contains:

<requirement type="package" version="1.0">python_nltk_tools</requirement>

and the tool_dependencies.xml file contains the definition:

<tool_dependency> <package name="python_nltk_tools" version="1.0"> ...

how do I tell planemo to tell galaxy that it should refer to this tool dependency file to resolve the requirement? At the moment it's loading all of the tools but doesn't seem to be concerned that the requirement isn't met.

Thanks for your help.

Steve

On 3 September 2015 at 18:06, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk> wrote:

...

Hi,

I wrote an extension that will help planemo pull in tool dependencies.

See https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/re...

It is for when the dependency was installed into galaxy but where planemo is not using the database to find that tool.

It works my helping planemo guess where the tool dependency may be.

Hope that helps. Christian University of Manchester ________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Steve Cassidy [steve.cassidy@mq.edu.au] Sent: Thursday, September 03, 2015 9:00 AM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] planemo and tool dependencies

Hi all, I'm trying to test some tools under planemo and can't find out how to have it install tool dependencies while setting up the environment.

The dependency is on a particular python module and we have a tool_dependencies.xml file to describe it. I can't see a way to tell planemo serve etc to refer to that file to get the dependencies.

Any help appreciated.

Steve

-- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

-- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

___________________________________________________________ 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/