Re: [galaxy-dev] Automatic installation of third party dependancies
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?... 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