Dear all, I'm currently testing a software package we developed for installation from the testtoolshed. Things seem to work fine mostly, but there is one thing I don't know how to solve (if it can be solved). Our package consists of 14 individual tools, which I uploaded as 14 separate repositories together with a repository suite definition that's taking care of installing all tools. Now, somewhat naively as it seems, I expected the order of repository declarations in the suite definition file to determine the order of the tools in the Galaxy Tools Bar, but, instead, they are added in seemingly random order. So I'm looking for a way to predefine the final order of the tools so that it makes sense for a typical workflow. Any advice how to address this? Thanks for your help, Wolfgang
Hi Wolfgang, You didn't include the name or a link to your Test Tool Shed packages. Are you talking about the suite_config.xml file? I'm not sure if Galaxy still uses that, no-one answered my earlier question: http://dev.list.galaxyproject.org/Role-of-suite-config-xml-in-current-Tool-S... https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020762.htm... e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/su... https://github.com/peterjc/pico_galaxy/issues/5 Peter On Wed, Dec 10, 2014 at 10:18 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:
Dear all,
I'm currently testing a software package we developed for installation from the testtoolshed. Things seem to work fine mostly, but there is one thing I don't know how to solve (if it can be solved).
Our package consists of 14 individual tools, which I uploaded as 14 separate repositories together with a repository suite definition that's taking care of installing all tools.
Now, somewhat naively as it seems, I expected the order of repository declarations in the suite definition file to determine the order of the tools in the Galaxy Tools Bar, but, instead, they are added in seemingly random order.
So I'm looking for a way to predefine the final order of the tools so that it makes sense for a typical workflow. Any advice how to address this?
Thanks for your help, Wolfgang
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Hi Peter, here's the link to the package: https://testtoolshed.g2.bx.psu.edu/view/wolma/suite_mimodd_0_1_5 It is not using a suite_config.xml file (which I hear of for the first time), but contains just a single repository_dependencies.xml file with this content: <?xml version="1.0"?> <repositories description="Metapackage for the installation of the MiModD suite of tools."> <repository changeset_revision="9be96af2cb36" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="9840b8f26be9" name="mimodd_fileinfo" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="666266c4e81f" name="mimodd_ngs_run_annotation" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="74993cc4af07" name="mimodd_convert" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="1ad8b72a9da8" name="mimodd_reheader" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="31e73b5e7278" name="mimodd_bamsort" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="2f47755c35da" name="mimodd_read_alignment" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="7330f7e114f4" name="mimodd_variant_calling" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="35215c432ad9" name="mimodd_extract_variants" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="92cdb9130d08" name="mimodd_coverage_stats" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="ed25fb216505" name="mimodd_deletion_prediction" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="3757a4ee201f" name="mimodd_vcf_filter" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="36c89c8d555b" name="mimodd_annotate_variants" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="818411f0ff39" name="mimodd_snpeff_genomes" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="3204016d5367" name="mimodd_cloudmap_prepare" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories> and I'd like Galaxy to add the corresponding tools in exactly this order to the Tools bar. Do I need an additional file to specify this order ? Best, Wolfgang On 12/10/2014 11:31 AM, Peter Cock wrote:
Hi Wolfgang,
You didn't include the name or a link to your Test Tool Shed packages. Are you talking about the suite_config.xml file?
I'm not sure if Galaxy still uses that, no-one answered my earlier question: http://dev.list.galaxyproject.org/Role-of-suite-config-xml-in-current-Tool-S... https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020762.htm...
e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/su... https://github.com/peterjc/pico_galaxy/issues/5
Peter
On Wed, Dec 10, 2014 at 10:18 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:
Dear all,
I'm currently testing a software package we developed for installation from the testtoolshed. Things seem to work fine mostly, but there is one thing I don't know how to solve (if it can be solved).
Our package consists of 14 individual tools, which I uploaded as 14 separate repositories together with a repository suite definition that's taking care of installing all tools.
Now, somewhat naively as it seems, I expected the order of repository declarations in the suite definition file to determine the order of the tools in the Galaxy Tools Bar, but, instead, they are added in seemingly random order.
So I'm looking for a way to predefine the final order of the tools so that it makes sense for a typical workflow. Any advice how to address this?
Thanks for your help, Wolfgang
___________________________________________________________ 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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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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Thanks Wolfgang, I think the suite_config.xml file was originally designed a subset of the tool_conf.xml file, inserted into it at run time. I think it could hold the tools in the desired order - probably with subsections and labels too. However, I suspect this may not be used with the current ToolShed setup - let's wait for the USA based Galaxy team to explain later today? Regards, Peter On Wed, Dec 10, 2014 at 10:40 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:
Hi Peter,
here's the link to the package:
https://testtoolshed.g2.bx.psu.edu/view/wolma/suite_mimodd_0_1_5
It is not using a suite_config.xml file (which I hear of for the first time), but contains just a single repository_dependencies.xml file with this content:
<?xml version="1.0"?> <repositories description="Metapackage for the installation of the MiModD suite of tools."> <repository changeset_revision="9be96af2cb36" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="9840b8f26be9" name="mimodd_fileinfo" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="666266c4e81f" name="mimodd_ngs_run_annotation" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="74993cc4af07" name="mimodd_convert" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="1ad8b72a9da8" name="mimodd_reheader" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="31e73b5e7278" name="mimodd_bamsort" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="2f47755c35da" name="mimodd_read_alignment" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="7330f7e114f4" name="mimodd_variant_calling" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="35215c432ad9" name="mimodd_extract_variants" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="92cdb9130d08" name="mimodd_coverage_stats" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="ed25fb216505" name="mimodd_deletion_prediction" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="3757a4ee201f" name="mimodd_vcf_filter" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="36c89c8d555b" name="mimodd_annotate_variants" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="818411f0ff39" name="mimodd_snpeff_genomes" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="3204016d5367" name="mimodd_cloudmap_prepare" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
and I'd like Galaxy to add the corresponding tools in exactly this order to the Tools bar. Do I need an additional file to specify this order ?
Best, Wolfgang
On 12/10/2014 11:31 AM, Peter Cock wrote:
Hi Wolfgang,
You didn't include the name or a link to your Test Tool Shed packages. Are you talking about the suite_config.xml file?
I'm not sure if Galaxy still uses that, no-one answered my earlier question:
http://dev.list.galaxyproject.org/Role-of-suite-config-xml-in-current-Tool-S...
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020762.htm...
e.g.
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/su... https://github.com/peterjc/pico_galaxy/issues/5
Peter
On Wed, Dec 10, 2014 at 10:18 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:
Dear all,
I'm currently testing a software package we developed for installation from the testtoolshed. Things seem to work fine mostly, but there is one thing I don't know how to solve (if it can be solved).
Our package consists of 14 individual tools, which I uploaded as 14 separate repositories together with a repository suite definition that's taking care of installing all tools.
Now, somewhat naively as it seems, I expected the order of repository declarations in the suite definition file to determine the order of the tools in the Galaxy Tools Bar, but, instead, they are added in seemingly random order.
So I'm looking for a way to predefine the final order of the tools so that it makes sense for a typical workflow. Any advice how to address this?
Thanks for your help, Wolfgang
___________________________________________________________ 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/
Peter - When you have previously asked about suite_config.xml I grepped around and I couldn't find any references to it, did some more greps just now and I still cannot. My best guess is that is not being used at all - but I am not a tool shed expert. Wolfgang - I am not aware of being able to enforce an ordering of these things. It would be a nice feature obviously so I have created a Trello card for the request - https://trello.com/c/lPOkD4BD. -John On Wed, Dec 10, 2014 at 6:08 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks Wolfgang,
I think the suite_config.xml file was originally designed a subset of the tool_conf.xml file, inserted into it at run time. I think it could hold the tools in the desired order - probably with subsections and labels too.
However, I suspect this may not be used with the current ToolShed setup - let's wait for the USA based Galaxy team to explain later today?
Regards,
Peter
On Wed, Dec 10, 2014 at 10:40 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:
Hi Peter,
here's the link to the package:
https://testtoolshed.g2.bx.psu.edu/view/wolma/suite_mimodd_0_1_5
It is not using a suite_config.xml file (which I hear of for the first time), but contains just a single repository_dependencies.xml file with this content:
<?xml version="1.0"?> <repositories description="Metapackage for the installation of the MiModD suite of tools."> <repository changeset_revision="9be96af2cb36" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="9840b8f26be9" name="mimodd_fileinfo" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="666266c4e81f" name="mimodd_ngs_run_annotation" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="74993cc4af07" name="mimodd_convert" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="1ad8b72a9da8" name="mimodd_reheader" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="31e73b5e7278" name="mimodd_bamsort" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="2f47755c35da" name="mimodd_read_alignment" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="7330f7e114f4" name="mimodd_variant_calling" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="35215c432ad9" name="mimodd_extract_variants" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="92cdb9130d08" name="mimodd_coverage_stats" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="ed25fb216505" name="mimodd_deletion_prediction" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="3757a4ee201f" name="mimodd_vcf_filter" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="36c89c8d555b" name="mimodd_annotate_variants" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="818411f0ff39" name="mimodd_snpeff_genomes" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="3204016d5367" name="mimodd_cloudmap_prepare" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
and I'd like Galaxy to add the corresponding tools in exactly this order to the Tools bar. Do I need an additional file to specify this order ?
Best, Wolfgang
On 12/10/2014 11:31 AM, Peter Cock wrote:
Hi Wolfgang,
You didn't include the name or a link to your Test Tool Shed packages. Are you talking about the suite_config.xml file?
I'm not sure if Galaxy still uses that, no-one answered my earlier question:
http://dev.list.galaxyproject.org/Role-of-suite-config-xml-in-current-Tool-S...
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020762.htm...
e.g.
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/su... https://github.com/peterjc/pico_galaxy/issues/5
Peter
On Wed, Dec 10, 2014 at 10:18 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:
Dear all,
I'm currently testing a software package we developed for installation from the testtoolshed. Things seem to work fine mostly, but there is one thing I don't know how to solve (if it can be solved).
Our package consists of 14 individual tools, which I uploaded as 14 separate repositories together with a repository suite definition that's taking care of installing all tools.
Now, somewhat naively as it seems, I expected the order of repository declarations in the suite definition file to determine the order of the tools in the Galaxy Tools Bar, but, instead, they are added in seemingly random order.
So I'm looking for a way to predefine the final order of the tools so that it makes sense for a typical workflow. Any advice how to address this?
Thanks for your help, Wolfgang
___________________________________________________________ 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/
On Wed, Dec 10, 2014 at 2:08 PM, John Chilton <jmchilton@gmail.com> wrote:
Peter -
When you have previously asked about suite_config.xml I grepped around and I couldn't find any references to it, did some more greps just now and I still cannot. My best guess is that is not being used at all - but I am not a tool shed expert.
Thanks John - that is my suspicion too, but I didn't try and go back over the hg logs to find out any more.
Wolfgang -
I am not aware of being able to enforce an ordering of these things. It would be a nice feature obviously so I have created a Trello card for the request - https://trello.com/c/lPOkD4BD.
-John
Great, I've subscribed to that issue too as this would be useful for things like the BLAST+ suite where it is nice to order the tools. Peter
On 10.12.2014 15:08, John Chilton wrote:
I am not aware of being able to enforce an ordering of these things. It would be a nice feature obviously so I have created a Trello card for the request - https://trello.com/c/lPOkD4BD.
Too bad this isn't possible yet, but thanks for adding the card. Just subscribed to it. Wolfgang
participants (3)
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John Chilton -
Peter Cock -
Wolfgang Maier