installable revisions for repository suite definitions

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installable revisions for repository suite definitions

Aaron Petkau
Hello,

I'm running into some issues with maintaining multiple installable revisions for a repository suite and I'm not sure if there's something I've missed.

I have a local toolshed where I'm maintaining my tools, and I have a repository suite definition, defining a number of dependencies.  So, I have:

suite_X (mercurial revision 0):
   Dependency A
   Dependency B

I updated "suite_X" and changed the dependencies:

suite_X (mercurial revision 1):
    Dependency A
    Dependency B
    Dependency C

I would like to have both mercurial revision 0 and 1 installable in Galaxy, but only revision 1 (the latest) is showing up as installable.  I found documentation at https://wiki.galaxyproject.org/RepositoryRevisions but this seems to only cover a repository containing a single tool, not a suite of tools.

Is there something I'm doing wrong or some setting I have to change here?  My toolshed is running with Galaxy tag "v15.07".

Thanks,

Aaron

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Re: installable revisions for repository suite definitions

Dave Bouvier
Aaron,

Repository suite definitions are designed to only allow the latest
revision to be installable. My recommendation in this case would be to
define two separate suites tagged in some descriptive way, so the
individual use cases would have their appropriate suites.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org

On 10/29/2015 02:23 PM, Aaron Petkau wrote:

> Hello,
>
> I'm running into some issues with maintaining multiple installable
> revisions for a repository suite and I'm not sure if there's something
> I've missed.
>
> I have a local toolshed where I'm maintaining my tools, and I have a
> repository suite definition, defining a number of dependencies.  So, I have:
>
> suite_X (mercurial revision 0):
>     Dependency A
>     Dependency B
>
> I updated "suite_X" and changed the dependencies:
>
> suite_X (mercurial revision 1):
>      Dependency A
>      Dependency B
>      Dependency C
>
> I would like to have both mercurial revision 0 and 1 installable in
> Galaxy, but only revision 1 (the latest) is showing up as installable.
> I found documentation at
> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
> only cover a repository containing a single tool, not a suite of tools.
>
> Is there something I'm doing wrong or some setting I have to change
> here?  My toolshed is running with Galaxy tag "v15.07".
>
> Thanks,
>
> Aaron
>
>
> ___________________________________________________________
> 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: installable revisions for repository suite definitions

Aaron Petkau
Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new suite with a version number in the name.

Another question, does the same apply for tool dependency definitions?  I've upgraded a suite of tools + dependency definitions, and now even if I make a new repository suite (to allow installing of my old set of tools, revision 0 in my example) it's installing the newer commit in one tool dependency definition repository.

Thanks,

Aaron

On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <[hidden email]> wrote:
Aaron,

Repository suite definitions are designed to only allow the latest revision to be installable. My recommendation in this case would be to define two separate suites tagged in some descriptive way, so the individual use cases would have their appropriate suites.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org


On 10/29/2015 02:23 PM, Aaron Petkau wrote:
Hello,

I'm running into some issues with maintaining multiple installable
revisions for a repository suite and I'm not sure if there's something
I've missed.

I have a local toolshed where I'm maintaining my tools, and I have a
repository suite definition, defining a number of dependencies.  So, I have:

suite_X (mercurial revision 0):
    Dependency A
    Dependency B

I updated "suite_X" and changed the dependencies:

suite_X (mercurial revision 1):
     Dependency A
     Dependency B
     Dependency C

I would like to have both mercurial revision 0 and 1 installable in
Galaxy, but only revision 1 (the latest) is showing up as installable.
I found documentation at
https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
only cover a repository containing a single tool, not a suite of tools.

Is there something I'm doing wrong or some setting I have to change
here?  My toolshed is running with Galaxy tag "v15.07".

Thanks,

Aaron


___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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Re: installable revisions for repository suite definitions

Martin Čech
Hi Aaron,


I believe that if you specify the repository_dependencies.xml of your suite in the following way:

<repositories>
<repository changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />

you will pin the exact revision of the tool (fasta_clipping_histogram here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and suite_fastx_toolkit_0_0_9 repositories which will install the requested versions of the tools.

M.

On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau <[hidden email]> wrote:
Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new suite with a version number in the name.

Another question, does the same apply for tool dependency definitions?  I've upgraded a suite of tools + dependency definitions, and now even if I make a new repository suite (to allow installing of my old set of tools, revision 0 in my example) it's installing the newer commit in one tool dependency definition repository.

Thanks,

Aaron

On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <[hidden email]> wrote:
Aaron,

Repository suite definitions are designed to only allow the latest revision to be installable. My recommendation in this case would be to define two separate suites tagged in some descriptive way, so the individual use cases would have their appropriate suites.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org


On 10/29/2015 02:23 PM, Aaron Petkau wrote:
Hello,

I'm running into some issues with maintaining multiple installable
revisions for a repository suite and I'm not sure if there's something
I've missed.

I have a local toolshed where I'm maintaining my tools, and I have a
repository suite definition, defining a number of dependencies.  So, I have:

suite_X (mercurial revision 0):
    Dependency A
    Dependency B

I updated "suite_X" and changed the dependencies:

suite_X (mercurial revision 1):
     Dependency A
     Dependency B
     Dependency C

I would like to have both mercurial revision 0 and 1 installable in
Galaxy, but only revision 1 (the latest) is showing up as installable.
I found documentation at
https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
only cover a repository containing a single tool, not a suite of tools.

Is there something I'm doing wrong or some setting I have to change
here?  My toolshed is running with Galaxy tag "v15.07".

Thanks,

Aaron


___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: installable revisions for repository suite definitions

Aaron Petkau
Thanks Martin, that helps me out.  However, the issue I'm running into is that it seems like specific revisions in my repository suite definition are being ignored and it's only using the latest one.

I think what may be happening is as follows.

In my repository suite I have a dependency like:

<repository changeset_revision="0" name="package_x" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />


Now, "package_x" defines dependencies for tools in a "tool_dependencies.xml" file.  And it has been updated to a newer revision, "1".

Looking through the toolshed, it looks like revision "0" for "package_x" isn't being set as an installable revision.  So, when installing my older repository dependency suite, it's ignoring revision "0" and just installing revision "1".

Is there any way to force it to install revision "0" of package_x?  Should I never be updating the repositories for tool dependencies?

This was all being tested out with toolshed tag "v15.05.1".

Thanks,

Aaron



On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech <[hidden email]> wrote:
Hi Aaron,


I believe that if you specify the repository_dependencies.xml of your suite in the following way:

<repositories>
<repository changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />

you will pin the exact revision of the tool (fasta_clipping_histogram here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and suite_fastx_toolkit_0_0_9 repositories which will install the requested versions of the tools.

M.

On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau <[hidden email]> wrote:
Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new suite with a version number in the name.

Another question, does the same apply for tool dependency definitions?  I've upgraded a suite of tools + dependency definitions, and now even if I make a new repository suite (to allow installing of my old set of tools, revision 0 in my example) it's installing the newer commit in one tool dependency definition repository.

Thanks,

Aaron

On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <[hidden email]> wrote:
Aaron,

Repository suite definitions are designed to only allow the latest revision to be installable. My recommendation in this case would be to define two separate suites tagged in some descriptive way, so the individual use cases would have their appropriate suites.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org


On 10/29/2015 02:23 PM, Aaron Petkau wrote:
Hello,

I'm running into some issues with maintaining multiple installable
revisions for a repository suite and I'm not sure if there's something
I've missed.

I have a local toolshed where I'm maintaining my tools, and I have a
repository suite definition, defining a number of dependencies.  So, I have:

suite_X (mercurial revision 0):
    Dependency A
    Dependency B

I updated "suite_X" and changed the dependencies:

suite_X (mercurial revision 1):
     Dependency A
     Dependency B
     Dependency C

I would like to have both mercurial revision 0 and 1 installable in
Galaxy, but only revision 1 (the latest) is showing up as installable.
I found documentation at
https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
only cover a repository containing a single tool, not a suite of tools.

Is there something I'm doing wrong or some setting I have to change
here?  My toolshed is running with Galaxy tag "v15.07".

Thanks,

Aaron


___________________________________________________________
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/


___________________________________________________________
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:
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Re: installable revisions for repository suite definitions

Martin Čech
Hi Aaron,

I think Galaxy will always install the latest revision of the selected installable revision. Our approach was that tool dependencies have versioned repositories (with versions in the names) so that it cannot happen that abyss 2.0 would be in the package_abyss_1_9_0 repo. With this in place you shouldn't care about the actual revision because it will always install correct version of the tool.

Carefuly following this fragile approach you should be able to achieve what you want. :/

Thank you.

M.



On Wed, Nov 4, 2015 at 1:09 PM Aaron Petkau <[hidden email]> wrote:
Thanks Martin, that helps me out.  However, the issue I'm running into is that it seems like specific revisions in my repository suite definition are being ignored and it's only using the latest one.

I think what may be happening is as follows.

In my repository suite I have a dependency like:

<repository changeset_revision="0" name="package_x" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />


Now, "package_x" defines dependencies for tools in a "tool_dependencies.xml" file.  And it has been updated to a newer revision, "1".

Looking through the toolshed, it looks like revision "0" for "package_x" isn't being set as an installable revision.  So, when installing my older repository dependency suite, it's ignoring revision "0" and just installing revision "1".

Is there any way to force it to install revision "0" of package_x?  Should I never be updating the repositories for tool dependencies?

This was all being tested out with toolshed tag "v15.05.1".

Thanks,

Aaron



On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech <[hidden email]> wrote:
Hi Aaron,


I believe that if you specify the repository_dependencies.xml of your suite in the following way:

<repositories>
<repository changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />

you will pin the exact revision of the tool (fasta_clipping_histogram here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and suite_fastx_toolkit_0_0_9 repositories which will install the requested versions of the tools.

M.

On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau <[hidden email]> wrote:
Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new suite with a version number in the name.

Another question, does the same apply for tool dependency definitions?  I've upgraded a suite of tools + dependency definitions, and now even if I make a new repository suite (to allow installing of my old set of tools, revision 0 in my example) it's installing the newer commit in one tool dependency definition repository.

Thanks,

Aaron

On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <[hidden email]> wrote:
Aaron,

Repository suite definitions are designed to only allow the latest revision to be installable. My recommendation in this case would be to define two separate suites tagged in some descriptive way, so the individual use cases would have their appropriate suites.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org


On 10/29/2015 02:23 PM, Aaron Petkau wrote:
Hello,

I'm running into some issues with maintaining multiple installable
revisions for a repository suite and I'm not sure if there's something
I've missed.

I have a local toolshed where I'm maintaining my tools, and I have a
repository suite definition, defining a number of dependencies.  So, I have:

suite_X (mercurial revision 0):
    Dependency A
    Dependency B

I updated "suite_X" and changed the dependencies:

suite_X (mercurial revision 1):
     Dependency A
     Dependency B
     Dependency C

I would like to have both mercurial revision 0 and 1 installable in
Galaxy, but only revision 1 (the latest) is showing up as installable.
I found documentation at
https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
only cover a repository containing a single tool, not a suite of tools.

Is there something I'm doing wrong or some setting I have to change
here?  My toolshed is running with Galaxy tag "v15.07".

Thanks,

Aaron


___________________________________________________________
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/


___________________________________________________________
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:
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Re: installable revisions for repository suite definitions

Aaron Petkau
Okay, that makes sense.  I'll switch over to making sure each tool dependency is in a separate repository with version names.  It was just one repo which we were updating a lot that ended up with multiple versions so it's an easy thing to do.

Thanks,

Aaron


On Wed, Nov 4, 2015 at 12:18 PM, Martin Čech <[hidden email]> wrote:
Hi Aaron,

I think Galaxy will always install the latest revision of the selected installable revision. Our approach was that tool dependencies have versioned repositories (with versions in the names) so that it cannot happen that abyss 2.0 would be in the package_abyss_1_9_0 repo. With this in place you shouldn't care about the actual revision because it will always install correct version of the tool.

Carefuly following this fragile approach you should be able to achieve what you want. :/

Thank you.

M.



On Wed, Nov 4, 2015 at 1:09 PM Aaron Petkau <[hidden email]> wrote:
Thanks Martin, that helps me out.  However, the issue I'm running into is that it seems like specific revisions in my repository suite definition are being ignored and it's only using the latest one.

I think what may be happening is as follows.

In my repository suite I have a dependency like:

<repository changeset_revision="0" name="package_x" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />


Now, "package_x" defines dependencies for tools in a "tool_dependencies.xml" file.  And it has been updated to a newer revision, "1".

Looking through the toolshed, it looks like revision "0" for "package_x" isn't being set as an installable revision.  So, when installing my older repository dependency suite, it's ignoring revision "0" and just installing revision "1".

Is there any way to force it to install revision "0" of package_x?  Should I never be updating the repositories for tool dependencies?

This was all being tested out with toolshed tag "v15.05.1".

Thanks,

Aaron



On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech <[hidden email]> wrote:
Hi Aaron,


I believe that if you specify the repository_dependencies.xml of your suite in the following way:

<repositories>
<repository changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />

you will pin the exact revision of the tool (fasta_clipping_histogram here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and suite_fastx_toolkit_0_0_9 repositories which will install the requested versions of the tools.

M.

On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau <[hidden email]> wrote:
Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new suite with a version number in the name.

Another question, does the same apply for tool dependency definitions?  I've upgraded a suite of tools + dependency definitions, and now even if I make a new repository suite (to allow installing of my old set of tools, revision 0 in my example) it's installing the newer commit in one tool dependency definition repository.

Thanks,

Aaron

On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <[hidden email]> wrote:
Aaron,

Repository suite definitions are designed to only allow the latest revision to be installable. My recommendation in this case would be to define two separate suites tagged in some descriptive way, so the individual use cases would have their appropriate suites.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org


On 10/29/2015 02:23 PM, Aaron Petkau wrote:
Hello,

I'm running into some issues with maintaining multiple installable
revisions for a repository suite and I'm not sure if there's something
I've missed.

I have a local toolshed where I'm maintaining my tools, and I have a
repository suite definition, defining a number of dependencies.  So, I have:

suite_X (mercurial revision 0):
    Dependency A
    Dependency B

I updated "suite_X" and changed the dependencies:

suite_X (mercurial revision 1):
     Dependency A
     Dependency B
     Dependency C

I would like to have both mercurial revision 0 and 1 installable in
Galaxy, but only revision 1 (the latest) is showing up as installable.
I found documentation at
https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
only cover a repository containing a single tool, not a suite of tools.

Is there something I'm doing wrong or some setting I have to change
here?  My toolshed is running with Galaxy tag "v15.07".

Thanks,

Aaron


___________________________________________________________
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/



___________________________________________________________
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/