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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