#56 Bugs in 1.0 Release

[Brian O'Connor]

These are the bugs that need to be fixed in a 1.1
release before the GMODWeb paper gets published. I'll
add more in comments to this post. Most are minor and
that's why I'm just creating one bug to track them all.

* GMODWeb
** feature template should check if < 0 in gimage
** search for ontology terms can produce blank page
** ontology template should not link to multiple root trees
** cv template should not try to display terms for bad
ontologies
** nice minor panel headers are missing e.g.
"Feature_Cvterm" should be "CV Terms" and the links
should be customized
** search for "YAL06*" and "YAL06" produce results but
the count is incorrect.

* Amigo Bugs
** amigo localhost set in config
** amigo embedded theme
** amigo details doesn't work
** amigo multi-node problem

I'll add more as they come up in the comments to this bug.

[Brian O'Connor]

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For search problems, modified:
* tt2/default/search.tt2
* lib/TurnkeySceS228C/Util/Search.pm

For GBrowse problem modified:
* tt2/custom/feature.tt2

[Brian O'Connor]

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For ontology display I edited:
* tt2/custom/cvterm.tt2
* tt2/custom/ontology_browser.tt2
to fix the problem of multi-root ontologies being rendered.

[Brian O'Connor]

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GBrowse page has error where it's passing in a source field,
should be removed in: tt2/custom/genome_browser.tt2