[galaxy-dev] picard and package_picard_1_56_0
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
XX --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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Re: [galaxy-dev] picard and package_picard_1_56_0
Evan,
Thank you for reporting this issue, it has now been corrected.
--Dave B.
On 11/11/2014 12:56 PM, Evan Bollig PhD wrote:
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
XX --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
___
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:
http://lists.bx.psu.edu/
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Is release_2014.10.06 official?
I see that the tags release_2014.10.06 and latest_2014.10.06 were created some time ago, but there was never any announcement. Are these considered officially released? Should I upgrade my instance to this version? Most importantly, are there any release notes so I can see what, if anything, I need to do to prepare for this update? Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] picard and package_picard_1_56_0
Thanks Dave,
Everything is back to normal again.
Cheers,
-E
-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
On Tue, Nov 11, 2014 at 2:20 PM, Dave Bouvier d...@bx.psu.edu wrote:
Evan,
Thank you for reporting this issue, it has now been corrected.
--Dave B.
On 11/11/2014 12:56 PM, Evan Bollig PhD wrote:
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
XX --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
___
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:
http://lists.bx.psu.edu/
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
