Devteam:

On 10/23 an update was posted to package_picard_1_56_0 that breaks
tool Picard. Since 10/23, picard depends on package_picard_1_56_0,
which in turn depends on picard 1.122.0, but that dependency makes
absolutely no sense.

Now when I run PairedReadMateFixer I get:
####################
## exit code=1; stdout=
Error: Unable to access jarfile /FixMateInformation.jar
####################
which appears to be caused by bad paths

I don't understand toolshed logic for revisions: when I install tools
with very specific revisions, the tool depends on very specific
revisions of other tools. However, when I install a tool that depends
on a package_*, the package has revision information, but it is
ignored in favor of installing the LATEST revision of the package. If
someone posts a buggy revision of a package_* to the toolshed, there
is no way to avoid installing it until a fixed version is posted in
its place.

For example, when I run:

python ./scripts/api/install_tool_shed_repositories.py --api
XXXXXXXXXX --local http://127.0.0.1:8080 --url
http://toolshed.g2.bx.psu.edu --name package_picard_1_56_0 --owner
devteam --revision 61e41d21cb6f --tool-deps --repository-deps
--panel-section-name "Other (Main Tool Shed)"'

I expect package_picard_1_56_0:61e41d21cb6f to be installed, but
instead I get package_picard_1_56_0:4a49481f29e7:

#######
Response
--------
/api/tool_shed_repositories/03501d7626bd192f
  name: package_picard_1_56_0
  status: Installed
  tool_shed_status: {u'latest_installable_revision': u'True',
u'revision_update': u'False', u'revision_upgrade': u'False',
u'repository_deprecated': u'False'}
  deleted: False
  ctx_rev: 1
  error_message:
  dist_to_shed: False
  tool_shed: toolshed.g2.bx.psu.edu
  installed_changeset_revision: 4a49481f29e7
  uninstalled: False
  owner: devteam
  changeset_revision: 4a49481f29e7
  id: 03501d7626bd192f
  includes_datatypes: False
#######

Why ignore the package revisions?

Btw, I did find an alternate (and working) package_picard_1_56_0 in
the test toolshed, but why do I need to depend on the test toolshed
for a production environment?

-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
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