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-Shed-tc4665887.html
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020762.html
e.g.
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/suite_config.xml
https://github.com/peterjc/pico_galaxy/issues/5
Peter
On Wed, Dec 10, 2014 at 10:18 AM, Wolfgang Maier
<[email protected]> 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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