I've run into this issue again, and I'm having a hard time working around it. However, I have confirmed that at least some updates to a tool in the tool shed will "invalidate" previously valid revisions and thus prevent users from installing or updating the tool at all.

For example, push version 0.1 of the tool and create a valid revision 1:xxxxxx. Then install the tool in galaxy. Make a small change (say to tool_dependencies.xml) and push a new revision (but keep the tool version the same), now at revision 2:xxxxxxx. The tool shed will show 2:xxxxxx as the only valid revision to install, but the galaxy system with revision 1:xxxxxx will be stuck, unable to get upgrades (Server Error described previously).

I'm trying to work around this now with my htseq-count tool, but so far no luck. I've created a few spurious revisions in the attempt, and I think now I may just try bumping the version (already did to no avail, toolshed still thinks it's the same) and uploading a tar file. That seems to more reliably parse metadata. Will let you know what, if anything, works. Thanks.

Lance

Greg Von Kuster wrote:
Hello Lance,

I've just committed a fix for getting updates to installed tool shed repositories in change set 7713:23107188eab8, which is currently available only in the Galaxy central repository. However, my fix will probably not correct the issue you're describing, and I'm still not able to reproduce this behavior. See my inline comments...


On Sep 13, 2012, at 4:41 PM, Lance Parsons wrote:

Actually, I think that is exactly the issue. I DO have 3:f7a5b54a8d4f installed. I've run into a related issue before, but didn't fully understand it.

I believe what happened was:
1) I pushed revision 3:f7a5b54a8d4f to the tool shed which contained the first revision of version 0.2 of the htseq-count tool. 2) I installed the htseq-count tool from the tool shed, getting revision 3:f7a5b54a8d4f 3) I pushed an update to version 0.2 of the htseq-count tool. The only changes were to tool-dependencies so I thought it would be safe to leave the version number alone (perhaps this is problem?)


You are correct in stating that the tool version number should not change just because you've added a tool_dependencies.xml file. This is definitely not causing the behavior you're describing.


4) I attempted to get updates and ran into the issue I described.

I also ran into this (I believe it was with freebayes, but not sure) when I removed (uninstalled) a particular revision of a tool. Then the tool was updated. I went to install and and it said that I already had a previous revision installed and should install that. However, I couldn't since the tool shed won't allow installation of old revisions of the same version of a tool.

The following section of the tool shed wiki should provide the details about why you are seeing this behavior. Keep in mind that you will only get certain updates to installed repositories from the tool shed. This behavior enables updates to installed tool versions. To get a completely new version of an installed tool (if one exists), you need to install a new (different) changeset revision from the tool shed repository.

http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance



Let me know if there is anything I can do to help sort this out.

Lance

Greg Von Kuster wrote:
Hi Lance,

What is the changeset revision that you installed? It looks like you could only have installed one of the following 3 revisions:

1:14e18dc9ed13 <http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=14e18dc9ed13&id=2df7e24ce6c1f224> 2:f5d08224af89 <http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=f5d08224af89&id=2df7e24ce6c1f224> 4:14bec14f4290 <http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=14bec14f4290&id=2df7e24ce6c1f224>

Since you could not have installed 3:f7a5b54a8d4f <http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=f7a5b54a8d4f&id=2df7e24ce6c1f224>, I'm not quite sure how you could be trying to update to 4. Did you install 4 and are trying to get updates?

I've tried several things but am not able to reproduce this behavior, so it's difficult to determine what may be causing the problem

Greg Von Kuster

On Sep 12, 2012, at 3:08 PM, Lance Parsons wrote:

I've updated my development system now, and when I try to get updates for that particular tool (htseq_count) I run into the following error. Any ideas on how I can/should fix this? Thanks.

URL: http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=f7a5b54a8d4f&latest_changeset_revision=14bec14f4290&latest_ctx_rev=4 <http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=f7a5b54a8d4f&latest_changeset_revision=14bec14f4290&latest_ctx_rev=4> File '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__
environ, self.app)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__
return self.app( environ, start_response )
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__
body = method( trans, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 184 in decorator
return func( self, trans, *args, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/controllers/admin_toolshed.py', line 1469 in update_to_changeset_revision
update_repository( repo, latest_ctx_rev )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util.py', line 1655 in update_repository
rev=ctx_rev )
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py', line 5661 in update
rev = scmutil.revsingle(repo, rev, rev).rev()
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 515 in revsingle
l = revrange(repo, [revspec])
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 588 in revrange
for r in m(repo, range(len(repo))):
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 1414 in mfunc
return getset(repo, subset, tree)
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 156 in getset
return methods[x[0]](repo, subset, *x[1:])
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 171 in symbolset
return stringset(repo, subset, x)
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 161 in stringset
x = repo[x].rev()
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py', line 235 in __getitem__
return context.changectx(self, changeid)
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py', line 103 in __init__
_("unknown revision '%s'") % changeid)
RepoLookupError: unknown revision '4'


Lance Parsons wrote:

Thanks Greg. I used you're updated version and added numpy as a
separate dependency. It seems to work in my development system. I
haven't updated my qa or production versions yet, so I can't check
there. Perhaps you could test it and let me know if there are issues, etc.

Glad I can be of help.

Lance

Greg Von Kuster wrote:

Hello Lance,

See my inline comments.


On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote:


I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not install properly. There are a couple of issues that I've run into.

1) The biggest issue is the inability to set both the PYTHONPATH and PATH environment variables as part of installation. If I put two separate<action type="set_environment"> tags, then the second overwrites the first in the env.sh file. If instead, I put two<environment_variable> tags within the action, only one (the second) gets executed during installation.


The above issues have been corrected in changeset 7621:108cda898646, which is currently available only in the Galaxy central repository. There is a new Galaxy distribution scheduled to go out today, but unfortunately this changeset will not be included. From here on, Galaxy releases are tentatively scheduled for every 2 weeks, so if you don't want to pull from the Galaxy central repository, the fix should be available in the next release 2 weeks from now.

I've slightly altered your tool_dependencies.xml file (mostly because I've implemented support for a new "make_directory" tag. It is attached below - you should updated your tool_dependencies.xml file in your htseq_count repository with this updated version.



2) Another issue is the inability to install Numpy as a dependancy to HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH when HTSeq is installed (or executed).


Were you attempting to install numpy as another package defined in your tool-dependencies.xml file? If so, the fixes in the above changeset should allow you to do that now since you can install it before htseq and set PYTHONPATH to point to numpy as part of the installation.

Let me know if you need additional help or bump into further problems. The tool dependency installation components are fairly immature, so adding enhancements for new tools like yours is very valuable.

Thanks for your help on this,

Greg Von Kuster



Any thoughts on how to address these issues would be appreciated.

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University



--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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