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