March 2010 - galaxy-dev - lists.galaxyproject.org

problem with getting the tables up in Profile Annotations
by CHAN Chee Seng 23 Apr '10

23 Apr '10

Hi, I have configured and built my own galaxy server. I have set up most of the genome databases but I have a problem with the getting the "Tables to Use" to be displayed on the web interface. I have looked at the following files. 1. annotation_profiler_options.xml 2. annotation_profiler_valid_builds.txt I did not change the annotation_profiler_options.xml file (used as is) and annotation_profiler_valid_builds.txt contains just one line, hg18 which is fine since I am starting with human. Where do I specify the location of my hg18? Please let me know if you need more information. Thanks for your help. Best regards, Chee Seng, Chan Genome Institute of Singapore 60 Biopolis Street, Genome #02-01 Singapore 138672 DID 64788065 ------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------------------------

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Issue with deleting multiple histories
by Tam, Oliver 15 Apr '10

15 Apr '10

Hi, I recently discovered an issue that prevents me from easily deleting multiple histories at once. This is the method I use: Click ³Options² on the right side menu -> Go to ³Saved Histories² -> Click on the check box of the history to be deleted -> Click ³Delete² button at the bottom (next to ³For selected histories:²). When I do this, nothing happens, and the history remains. However, if I click on the the downward triangle and click on ³Delete² from the pull down menu, the history is correctly deleted. Deleting using the check-boxes and the Delete button works in changeset 3446:143c920af25c But fails in changeset 3447:f5d383525d68. Please let me know if you cannot reproduce the problem. Cheers, Oliver

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run.sh paste error
by Nathaniel Street 14 Apr '10

14 Apr '10

Hi I have a problem that I've not been able to track down. I've tried searching the mailing list archive and googling. When I enable paste in universe_wsgi.ini and then run run.sh I get this error. The same occurs for both the stable and development branches. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 274, in command relative_to=base, global_conf=vars) File "/home/nat/work/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 308, in loadserver relative_to=relative_to, **kw) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 210, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 409, in get_context section) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 431, in _context_from_use object_type, name=use, global_conf=global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 361, in get_context global_conf=global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 285, in _loadegg return loader.get_context(object_type, name, global_conf) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 561, in get_context object_type, name=name) File "/home/nat/work/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 600, in find_egg_entry_point for prot in protocol_options] or '(no entry points)')))) LookupError: Entry point 'gzip' not found in egg 'Paste' (dir: /home/nat/work/software/galaxy-central/eggs/Paste-1.6-py2.6.egg; protocols: paste.server_factory, paste.server_runner; entry_points: ) The strange thing is on another machine I don't get the error but I can't find out what the missing dependency is on the machine the generates the error despite comparing installed packages etc. I'm running Ubunutu 9.1 64bit on both machines. Can anyone tell me what I'm missing that leads to the above error? Many thanks Nathaniel -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org

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Re: [galaxy-dev] Weird problem with importing datasets
by Chris Cole 13 Apr '10

13 Apr '10

On 09/03/10 15:42, Chris Cole wrote: > On 09/03/10 14:53, Nate Coraor wrote: >> Chris Cole wrote: >>> Anyone got any ideas on this? >>> >>> It's still not working (following the most recent updates) and we've >>> got some NGS data to import into Galaxy. >> >> Hi Chris, >> >> To use this feature, the contents of library_import_dir should >> themselves be directories (or symlinks to the same). Selecting that >> directory from the dropdown in the library upload form will then import >> the contents of those directories. > > Ah, right. That's not clear in the docs. > > How come it works with locally symlinked files, then? Just checked it again (sorry I shouldn't have sent the previous email) with a directory and it still isn't working. www-galaxy@ge-002: tmp> cd ~/data_import/ www-galaxy@ge-002: data_import> ls README www-galaxy@ge-002: data_import> ln -s /homes/pschofield/data/TOH www-galaxy@ge-002: data_import> ls TOH/ 0min_1.txt 30m_1.txt 60min_1.txt Cd_inuc_1.txt Cmono_1.txt Dd_inuc_1.txt Dmono_1.txt processed 0min_2.txt 30m_2.txt 60min_2.txt Cd_inuc_2.txt Cmono_2.txt Dd_inuc_2.txt Dmono_2.txt www-galaxy@ge-002: data_import> ls -l total 96 -rw-r--r-- 1 www-galaxy barton 142 Mar 9 14:14 README lrwxrwxrwx 1 www-galaxy barton 26 Mar 9 15:59 TOH -> /homes/pschofield/data/TOH I got the TOH option in the 'Upload directory of files', which I selected, but the upload failed. Again, this is the error I get when selecting one of the filenames in the dataset: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error Thanks for help. Chris

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Wiki Addition: Site Map and Site Index
by Kelly Vincent 06 Apr '10

06 Apr '10

Everyone, Bitbucket (our code and wiki host) does not offer any way to search the wiki, so there are now two new pages to fill the void: SiteMap and SiteIndex. These are both generated automatically. The idea is that the pages should be generated by a script that is scheduled to run each night, but I'm still getting that going--in the meantime, I'll be running the script manually. SiteMap is a simple listing of all the pages found under the base wiki directory. You can get a pretty good idea what the page is about just by the name of it, which is all that's included in this list. You can see SiteMap at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap. SiteIndex is more complicated. It is a traditional index, which means that (almost) every word that appears in the wiki is included with a list of the pages on which it appears following it. A stoplist was used to remove useless or meaningless words, but there is still some junk that has made it past this filter. The index involves multiple pages, divided up alphabetically. It's available at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteIndex . Regards, Kelly

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change_format and conditonal vars
by Edward Kirton 05 Apr '10

05 Apr '10

hi, how do i reference conditional variables from within the change_format tag? i couldn't find any examples that did this. an example tool config xml file follows. thanks! ed kirton us doe jgi <tool id="fasta_get_seqs" name="Get Sequences"> <description>Create a Fasta/Qual file of selected sequences</description> <command interpreter="perl">fasta_get_seqs.pl $intype.infile $input_table $id_column $ignorecase $cosorted $output #for $i in $filters "${i.condition} ${i.column} ${i.value}" #end for </command> <inputs> <conditional name='intype'> <param name='sel' type='select' label='Input file type'> <option value='Fasta'>Fasta</option> <option value='Qual454'>Qual454</option> </param> <when value='Fasta'> <param name="infile" type="data" format="fasta" label="Fasta file"/> </when> <when value='Qual454'> <param name="infile" type="data" format="qual454" label="Qual454 file"/> </when> </conditional> <param name="input_table" type="data" format="tabular" label="File containing target IDs"/> <param name='id_column' type='data_column' data_ref='input_table' label='Column containing sequence IDs'/> <param name='ignorecase' type='boolean' truevalue='1' falsevalue='0' label='Ignore case?' /> <param name="cosorted" type="boolean" checked="true" truevalue='1' falsevalue='0' label='Sequences appear in same order in both files'/> <repeat name='filters' title='Filter'> <param name='condition' type='select' label='Condition'> <option value='s_eq'>text equals</option> <option value='s_ne'>text not equals</option> <option value='s_contains'>text contains</option> <option value='s_startswith'>text starts with</option> <option value='s_endswith'>text ends with</option> <option value='n_eq'>number ==</option> <option value='n_ne'>number !=</option> <option value='n_gt'>number ></option> <option value='n_lt'>number <</option> </param> <param name='column' type='data_column' data_ref='input_table' label='On column'/> <param name='value' type='text' label='Value'/> </repeat> </inputs> <outputs> <data name="output" format="fasta"> <change_format> <when input="intype.sel" value="Qual454" format="qual454" /> </change_format> </data> </outputs> <help> **What it does** Produces a Fasta/Qual file of selected sequences. If the files are cosorted, a much faster algorithm is used. If it fails, it assumes the files were not cosorted and automatically tries again using the slower algorithm which does not require cosorted files. One or more filters may be included to evaluate text (equal, not equal, contains, starts with) or numeric data (==, !=, >, <). </help> </tool>

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Patch: show User menu's history and dataset options show independent of app.config.use_remote_user setting
by Ry4an Brase 30 Mar '10

30 Mar '10

It's not much, but we're using a remote_user setup and the History and Datasets menu items were not showing up under the User menu, which didn't seem to be by design. Attached is a micro patch to the template, which is also available here: http://bitbucket.org/Ry4an/galaxy-umn-msi-changes/src/tip/always-show-users… Also, What's the preferred patch submission mechanism? Patchbomb? Bitbucket pull-request? Thanks, -- Ry4an Brase 612-626-6575 University of Minnesota Supercomputing Institute for Advanced Computational Research http://www.msi.umn.edu

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'Never ending' jobs in history
by Chris Cole 26 Mar '10

26 Mar '10

Hi, Occasionally, we see jobs that are constantly in the 'job running' state in the history. This is despite the fact that the job completed correctly. I can also see in the paster.log file that Galaxy has picked up on the fact that the job ended, but it just hasn't updated the UI. Clicking the eye for the 'running' history items does show the results of the run. This does not happen all the time. Is this a known issue and/or how can I resolve it? Thanks, Chris

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Re: [galaxy-dev] Python crashing after latest changeset update (OSX) (Fixed)
by Roy Weckiewicz 25 Mar '10

25 Mar '10

Solved this problem by creating a new instance of galaxy via hg clone and creating a new MySQL database followed by the setup.sh, modifying universe_wsgi.ini to point to my MySQL database and finally run.sh which migrated the database and started the server without a Python crash. On Thu, Mar 25, 2010 at 4:35 PM, Roy Weckiewicz <roystefan(a)gmail.com> wrote: > Hello, > > > After doing a hg pull and update a few minutes ago, my Python (2.5.1) is > crashing on OSX (10.5.8) after I run.sh daemon. The galaxy log doesn't seem > to contain any information about the error and seems to start the galaxy > server just fine (localhost). I've attached osx error report details. Any > ideas? > > > > > Thank you, > > > Roy Weckiewicz > > -- > Roy Weckiewicz > Texas A&M University > -- Roy Weckiewicz Texas A&M University

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Python crashing after latest changeset update (OSX)
by Roy Weckiewicz 25 Mar '10

25 Mar '10

Hello, After doing a hg pull and update a few minutes ago, my Python (2.5.1) is crashing on OSX (10.5.8) after I run.sh daemon. The galaxy log doesn't seem to contain any information about the error and seems to start the galaxy server just fine (localhost). I've attached osx error report details. Any ideas? Thank you, Roy Weckiewicz -- Roy Weckiewicz Texas A&M University

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