Heh, always something that's discovered after the fact. Happens to me all the time. Thanks for getting back to me quickly. Looks like the fix you did works. Only other tool is sam_to_bam https://toolshed.g2.bx.psu.edu/repository?repository_id=01221a8c57f0fc1a&changeset_revision=c73bf16b45df. Hopefully not too much trouble. Thanks again Martin, Aaron On Wed, Aug 12, 2015 at 5:10 PM, Martin Čech <marten@bx.psu.edu> wrote:

Hi Aaron,

this is most probably connected with a bug that we discovered today in the 'reset metadata for all my repositories' feature. Unfortunately we discovered it by running it on Main Tool Shed. We have an alternate (time consuming) way of fixing individual repos (like I just did for the samtools_mpileup) so if you give me a list of tools you need to use with old revisions I will make sure they are in a good shape.

This only affects devteam repos. We are working on a fix, please bare with us.

Thank you for using Galaxy!

Martin

On Wed, Aug 12, 2015 at 5:44 PM Aaron Petkau <aaron.petkau@gmail.com> wrote:

...

Hey everyone,

So I rely a lot on specific versions of tools in the toolshed, and am often testing out the install process to make sure everything's working. Today I noticed that my install process was failing, and it looks like it's due to not being able to install previous versions of tools through the API. It seems to default to installing the latest version of a tool.

For example, for the tool samtools_mpileup <https://toolshed.g2.bx.psu.edu/repository?repository_id=01d08a1b766b864e&changeset_revision=aa0ef6f0ee89>, if I run the code:

gi.toolShed.install_repository_revision("http://toolshed.g2.bx.psu.edu/ ",'samtools_mpileup','devteam','973fea5b4bdf',install_tool_dependencies=True,install_repository_dependencies=True)

in bioblend (to install revision 973fea5b4bdf) I instead get the latest (aa0ef6f0ee89) revision installed. I can see the previous revision still exists https://toolshed.g2.bx.psu.edu/repository?repository_id=01d08a1b766b864e&changeset_revision=973fea5b4bdf .

I'm wondering if something has changed here? I remember being able to install old versions of tools through the API before, but maybe I'm getting mixed up?

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/

Hello Martin, Yep, this is fully resolved for me. Thanks for following up, and for all the hard work you and the rest of the team do. Aaron On Fri, Aug 21, 2015 at 9:55 AM, Martin Čech <marten@bx.psu.edu> wrote:

Hi Aaron,

I am just following up with a note that this has been fully resolved. Please let us know if you find any more problems.

Thank you for using Galaxy.

Martin

On Wed, Aug 12, 2015 at 7:21 PM Aaron Petkau <aaron.petkau@gmail.com> wrote:

...

Heh, always something that's discovered after the fact. Happens to me all the time. Thanks for getting back to me quickly. Looks like the fix you did works. Only other tool is sam_to_bam https://toolshed.g2.bx.psu.edu/repository?repository_id=01221a8c57f0fc1a&changeset_revision=c73bf16b45df. Hopefully not too much trouble.

Thanks again Martin,

Aaron On Wed, Aug 12, 2015 at 5:10 PM, Martin Čech <marten@bx.psu.edu> wrote:

...

Hi Aaron,

this is most probably connected with a bug that we discovered today in the 'reset metadata for all my repositories' feature. Unfortunately we discovered it by running it on Main Tool Shed. We have an alternate (time consuming) way of fixing individual repos (like I just did for the samtools_mpileup) so if you give me a list of tools you need to use with old revisions I will make sure they are in a good shape.

This only affects devteam repos. We are working on a fix, please bare with us.

Thank you for using Galaxy!

Martin

On Wed, Aug 12, 2015 at 5:44 PM Aaron Petkau <aaron.petkau@gmail.com> wrote:

...

Hey everyone,

So I rely a lot on specific versions of tools in the toolshed, and am often testing out the install process to make sure everything's working. Today I noticed that my install process was failing, and it looks like it's due to not being able to install previous versions of tools through the API. It seems to default to installing the latest version of a tool.

For example, for the tool samtools_mpileup <https://toolshed.g2.bx.psu.edu/repository?repository_id=01d08a1b766b864e&changeset_revision=aa0ef6f0ee89>, if I run the code:

gi.toolShed.install_repository_revision("http://toolshed.g2.bx.psu.edu/ ",'samtools_mpileup','devteam','973fea5b4bdf',install_tool_dependencies=True,install_repository_dependencies=True)

in bioblend (to install revision 973fea5b4bdf) I instead get the latest (aa0ef6f0ee89) revision installed. I can see the previous revision still exists https://toolshed.g2.bx.psu.edu/repository?repository_id=01d08a1b766b864e&changeset_revision=973fea5b4bdf .

I'm wondering if something has changed here? I remember being able to install old versions of tools through the API before, but maybe I'm getting mixed up?

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/