Dear, We are running Galaxy on our local server(linux 64 bit) and try to upload a file (fasta, fastq) to the application. This returns the following error: Traceback (most recent call last): File "/data/home/joris/galaxy_dist/tools/data_source/upload.py", line 10, in import galaxy.model File "/data/home/joris/galaxy_dist/lib/galaxy/model/__init__.py", line 13, in import galaxy.datatypes.registry File "/data/home/joris/galaxy_dist/lib/galaxy/datatypes/registry.py", line 6, in import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo File "/data/home/joris/galaxy_dist/lib/galaxy/datatypes/data.py", line 6, in import metadata File "/data/home/joris/galaxy_dist/lib/galaxy/datatypes/metadata.py", line 5, in from galaxy.web import form_builder File "/data/home/joris/galaxy_dist/lib/galaxy/web/__init__.py", line 5, in from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder File "/data/home/joris/galaxy_dist/lib/galaxy/web/framework/__init__.py", line 30, in pkg_resources.require( "SQLAlchemy >= 0.4" ) File "/data/home/joris/galaxy_dist/lib/galaxy/eggs/__init__.py", line 544, in require sys.path.remove(entry) ValueError: list.remove(x): x not in list Do you know how this error can be solved? I hope to hear from you soon. Sincerely, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Dijk, F van wrote:
We are running Galaxy on our local server(linux 64 bit) and try to upload a file (fasta, fastq) to the application. This returns the following error:
Hi Freerk, This is a bug in our Python dependency handling code. Do you have a copy of SQLAlchemy installed in your $PYTHONPATH or in your Python's site-packages? Something about the way it's installed is causing our version conflict code to fail to find and override it. This bug has been floating around for a while and I'm never able to cause such conflicts myself, so it's been difficult to fix. The quick solution is to remove the conflicting copy of SQLAlchemy, but if you can spare me a few minutes to troubleshoot, that would be a great help. Thanks, --nate
On Tue, 2009-10-27 at 10:29 -0400, Nate Coraor wrote:
Dijk, F van wrote:
We are running Galaxy on our local server(linux 64 bit) and try to upload a file (fasta, fastq) to the application. This returns the following error:
Hi Freerk,
This is a bug in our Python dependency handling code. Do you have a copy of SQLAlchemy installed in your $PYTHONPATH or in your Python's site-packages? Something about the way it's installed is causing our version conflict code to fail to find and override it.
This bug has been floating around for a while and I'm never able to cause such conflicts myself, so it's been difficult to fix. The quick solution is to remove the conflicting copy of SQLAlchemy, but if you can spare me a few minutes to troubleshoot, that would be a great help.
Thanks, --nate _______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
Hi Nate, I am having the same problem. Here is the traceback, on python 2.5.4, with no sqlalchemy in python's path:
Traceback (most recent call last): File "/var/www/galaxy-dev/tools/data_source/upload.py", line 10, in import galaxy.model File "/var/www/galaxy-dev/lib/galaxy/model/__init__.py", line 13, in import galaxy.datatypes.registry File "/var/www/galaxy-dev/lib/galaxy/datatypes/registry.py", line 6, in import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo File "/var/www/galaxy-dev/lib/galaxy/datatypes/data.py", line 6, in import metadata File "/var/www/galaxy-dev/lib/galaxy/datatypes/metadata.py", line 5, in from galaxy.web import form_builder File "/var/www/galaxy-dev/lib/galaxy/web/__init__.py", line 5, in from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder File "/var/www/galaxy-dev/lib/galaxy/web/framework/__init__.py", line 10, in import base File "/var/www/galaxy-dev/lib/galaxy/web/framework/base.py", line 16, in pkg_resources.require( "WebOb" ) File "/var/www/galaxy-dev/lib/galaxy/eggs/__init__.py", line 553, in require sys.path.remove(entry) ValueError: list.remove(x): x not in list
This is while uploading a solexa fastq file *or* a fasta file *or* a GFF 3 file. In fact, I assume it will happen with any kind of file via the upload tool. It only happens with latest batch of revisions. Those were quite a few: I don't know my way around mercurial enough to be able to check which was the previous revision just before my last pull/update; if you know how I'll be happy to let you know which one it was. Looking at the log, this looks like a fist problem, right before all others cascade (then again, it might not have anything to do with it):
galaxy.tools DEBUG 2009-10-29 10:19:49,752 Loading section: FASTA/Q Information galaxy.datatypes.registry WARNING 2009-10-29 10:19:49,752 unknown extension in data factory fastqsanger
Then comes this:
galaxy.tools ERROR 2009-10-29 10:17:37,406 error reading tool from path: fastx_toolkit/fastq_qual_stat.xml [snip] galaxy.tools ERROR 2009-10-29 10:19:49,823 error reading tool from path: fastx_toolkit/fastq_nucleotides_distribution.xml Traceback (most recent call last): File "/var/www/galaxy-dev/lib/galaxy/tools/__init__.py", line 73, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/var/www/galaxy-dev/lib/galaxy/tools/__init__.py", line 127, in load_tool tree = util.parse_xml( config_file ) File "/var/www/galaxy-dev/lib/galaxy/util/__init__.py", line 101, in parse_xml tree = ElementTree.parse(fname) File "/var/www/galaxy-dev/eggs/py2.5-noplatform/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/var/www/galaxy-dev/eggs/py2.5-noplatform/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_nucleotides_distribution.xml' galaxy.tools DEBUG 2009-10-29 10:19:49,824 Loading section: FASTA/Q Preprocessing galaxy.datatypes.registry WARNING 2009-10-29 10:19:49,825 unknown extension in data factory fastq galaxy.tools ERROR 2009-10-29 10:19:49,838 error reading tool from path: fastx_toolkit/fastq_qual_conv.xml [snip]
which I removed by doing
ln -s $GALAXYROOT/tools/fastx_toolkit/fastx_quality_statistics.xml $GALAXYROOT/tools/fastx_toolkit/fastq_qual_stat.xml ln -s $GALAXYROOT/tools/fastx_toolkit/fastx_nucleotides_distribution.xml $GALAXYROOT/tools/fastx_toolkit/fastq_nucleotides_distribution.xml ln -s $GALAXYROOT/tools/fastx_toolkit/fastq_quality_converter.xml $GALAXYROOT/tools/fastx_toolkit/fastq_qual_conv.xml
since those files don't exist, and similar sounding ones do. This might be a mistake, but it was worth a try. Didn't work though. I still get the first traceback when uploading files. I'm out of ideas. Thanks for any help. Pedro -- Pedro Silva <pedros@berkeley.edu> UC Berkeley - PMB
Pedro Silva wrote:
I am having the same problem. Here is the traceback, on python 2.5.4, with no sqlalchemy in python's path:
File "/var/www/galaxy-dev/lib/galaxy/web/framework/base.py", line 16, in pkg_resources.require( "WebOb" ) File "/var/www/galaxy-dev/lib/galaxy/eggs/__init__.py", line 553, in require sys.path.remove(entry) ValueError: list.remove(x): x not in list
Hi Pedro, In your case, it looks like the conflicting egg is WebOb. Does it exist in your sys.path anywhere?
This is while uploading a solexa fastq file *or* a fasta file *or* a GFF 3 file. In fact, I assume it will happen with any kind of file via the upload tool.
This should be the case, yes.
galaxy.tools ERROR 2009-10-29 10:17:37,406 error reading tool from path: fastx_toolkit/fastq_qual_stat.xml [snip] galaxy.tools ERROR 2009-10-29 10:19:49,823 error reading tool from path: fastx_toolkit/fastq_nucleotides_distribution.xml Traceback (most recent call last): File "/var/www/galaxy-dev/lib/galaxy/tools/__init__.py", line 73, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/var/www/galaxy-dev/lib/galaxy/tools/__init__.py", line 127, in load_tool tree = util.parse_xml( config_file ) File "/var/www/galaxy-dev/lib/galaxy/util/__init__.py", line 101, in parse_xml tree = ElementTree.parse(fname) File "/var/www/galaxy-dev/eggs/py2.5-noplatform/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/var/www/galaxy-dev/eggs/py2.5-noplatform/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_nucleotides_distribution.xml' galaxy.tools DEBUG 2009-10-29 10:19:49,824 Loading section: FASTA/Q Preprocessing galaxy.datatypes.registry WARNING 2009-10-29 10:19:49,825 unknown extension in data factory fastq galaxy.tools ERROR 2009-10-29 10:19:49,838 error reading tool from path: fastx_toolkit/fastq_qual_conv.xml [snip]
which I removed by doing
ln -s $GALAXYROOT/tools/fastx_toolkit/fastx_quality_statistics.xml $GALAXYROOT/tools/fastx_toolkit/fastq_qual_stat.xml ln -s $GALAXYROOT/tools/fastx_toolkit/fastx_nucleotides_distribution.xml $GALAXYROOT/tools/fastx_toolkit/fastq_nucleotides_distribution.xml ln -s $GALAXYROOT/tools/fastx_toolkit/fastq_quality_converter.xml $GALAXYROOT/tools/fastx_toolkit/fastq_qual_conv.xml
since those files don't exist, and similar sounding ones do. This might be a mistake, but it was worth a try. Didn't work though. I still get the first traceback when uploading files.
If you haven't copied your tool config (tool_conf.xml) from the distribution (tool_conf.xml.sample) lately, you might want to do that now, which should fix these errors. Don't forget to copy any local changes (if any) to the new config. --nate
On Thu, 2009-10-29 at 14:20 -0400, Nate Coraor wrote:
Hi Pedro,
In your case, it looks like the conflicting egg is WebOb. Does it exist in your sys.path anywhere?
[snip]
If you haven't copied your tool config (tool_conf.xml) from the distribution (tool_conf.xml.sample) lately, you might want to do that now, which should fix these errors. Don't forget to copy any local changes (if any) to the new config.
--nate
Thanks Nate, Removing webob, simplejson, pastedeploy, and a few other things did the trick. Do you guys plan on ever letting the system resolve dependencies itself, or are you always going to keep using eggs for self-contained packages? Pedro
Pedro Silva wrote:
Removing webob, simplejson, pastedeploy, and a few other things did the trick. Do you guys plan on ever letting the system resolve dependencies itself, or are you always going to keep using eggs for self-contained packages?
Hi Pedro, Because Galaxy depends on very specific versions of these dependencies, allowing any system-installed version would raise a whole host of difficult to decipher problems. Although the 'require' code is supposed to specifically handle dependency conflicts like this, it clearly does not work in all cases. I'm unable to find a configuration which causes this issue locally, however, so I haven't been able to track down the bug yet. --nate
participants (3)
-
Dijk, F van -
Nate Coraor -
Pedro Silva