February 2014 - galaxy-dev - lists.galaxyproject.org

Error when installing package_galaxy_utils
by Sarah Diehl 25 Feb '14

25 Feb '14

Hi everyone, I just updated our local Galaxy installation to the latest dist version and also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh). However, the package galaxy_utils gave me an error and I don't have the slightest idea what happened. So any help to figure out the issue is greatly appreciated! Thanks, Sarah ############################################# export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python && python setup.py install --home /galaxy/galaxy_data/tools/galaxy_seq uence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7 STDERR Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz Extracting in /tmp/tmpo9Zxdz Now working in /tmp/tmpo9Zxdz/distribute-0.6.38 Building a Distribute egg in /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0 /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg error: site.py: Resource temporarily unavailable #############################################

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Optional multiple file selectors,
by Peter Cock 25 Feb '14

25 Feb '14

Hi John, As you noticed (and posted on Twitter), I've just tweaked the NCBI makeblastdb wrapper on GitHub to use a multiple file picker instead of a repeat: https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687… That seems to be working fine in human testing (although not on the functional side). I've also just tried this for the masking files - but ran into a problem. Here the masks are optional, and I want the default to be no mask: https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54c… This works fine from the user interface perspective: <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" /> This requires at least one file, although a confusing red error message is given if none is selected: "History does not include a dataset of the required format / build" <param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> This does not require a file, and defaults to selecting a new dummy entry "Selection is Optional". This is presumably intended as a visual cue - but it means you can do weird things like picking a read file and the dummy entry, or no entries. Neither allows me to proceed, instead on pressing execute I get a red error on a new page: Error executing tool: 'NoneType' object has no attribute 'file_name' galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while attempting tool execution: Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1916, in __handle_tool_execute _, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 2424, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py", line 287, in execute data.name = self.get_output_name( output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 26, in params self.wrap_values( self.tool.inputs, params, skip_missing_values=not self.tool.check_values ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 51, in wrap_values name=input.name ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 215, in __init__ list.__init__( self, map( to_wrapper, datasets ) ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 209, in to_wrapper real_path = dataset.file_name AttributeError: 'NoneType' object has no attribute 'file_name' Any thoughts? Is zero files a little tested corner of the multiple file support? If I have a suitable masking file in my history, and I select it, the tool runs fine. Thanks, Peter

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Rendering of multi-selection list
by Michael Römer 25 Feb '14

25 Feb '14

Hi everyone, I'm using the following xml syntax to populate a multi-selection list in our Galaxy Server: <param name="genes" type="select" label="Some list" multiple="true"> <options from_file="some_list.txt"> <column name="value" index="0" /> <column name="name" index="0" /> </options> </param> Depending on the number of entries in the file some_list.txt the list is rendered differently: * with less than 20 entries I get a list displaying all items * with more than 20 entries the list is rendered as a drop-down list * with a lot more (I don't know the exact cutoff, but like 1000+) I get the same rendering as with less than 20 entries I would like galaxy to render the list as a drop-down list independent of the number of entries. Is there a way to do this? Regards, Michael -- Michael Römer, MSc. Bioinf. Abteilung Kognitive Systeme Fachbereich Informatik Wilhelm-Schickard-Institut Sand 1, Raum A312 72076 Tübingen Tel.: +497071/2978970 E-Mail: michael.roemer(a)uni-tuebingen.de

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Test Tool Shed, nightly tests: Error 'unicode' object has no attribute 'get'
by Peter Cock 25 Feb '14

25 Feb '14

Hi guys, Yesterday I made a small tweak to the BLAST+ packages to fix a bash syntax error in the fall back action: https://github.com/peterjc/galaxy_blast/commit/4b2fa1fbf485c4630cb6dc0beaf7… I uploaded this update to the Test Tool Shed packages (all four, BLAST+ 2.2.26, 2.2.27, 2.2.28 and 2.2.29), most of which now unfortunately all show up under "Latest revision: installation errors" (along with the BLAST+ wrappers): Name↓Latest Installable RevisionOwnerncbi_blast_plus<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 39:22b7cdcf4960 (2014-02-20) peterjcpackage_blast_plus_2_2_26<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 5:ebde5fa60194 (2014-02-20) iucpackage_blast_plus_2_2_28<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 2:6f6a8be93479 (2014-02-20) iucpackage_blast_plus_2_2_29<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 1:c021862e9ea8 (2014-02-20) iuc The BLAST+ 2.2.26 package doesn't seem to show an error: Automated tool test results Test runs 2014-02-20 07:58:47 Tool dependencies TypeNameVersion blast+ package 2.2.26+ Error None The BLAST+ 2.2.27 package seems to have no test results at all. However, the BLAST+ 2.2.28 package has this strange unicode error: Automated tool test results Test runs 2014-02-20 12:48:52 This repository Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' And similarly for BLAST+ 2.2.29, Automated tool test results Test runs 2014-02-20 14:37:58 This repository Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' This is puzzling, since the changes I made to the packages seemed innocuous - making me wonder if something changed in the Test Tool Shed itself? Regards, Peter

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Unicode error manipulation of fastq
by Cantarel, Brandi L. 24 Feb '14

24 Feb '14

Hi, I am testing my newly installed galaxy instance. When I try to use a simple tool like fastq_to_fasta, I get the following error: UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in position 693: ordinal not in range(256) Anyone know how I can fix this? Thanks! Brandi ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) ********************************************************************** This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information.

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Unexpected behaviour when downloading HTML files
by Shian Su 24 Feb '14

24 Feb '14

Hello, After updating my local Galaxy instance to the latest stable release, I've noticed that clicking the floppy-disk download icon on a history item of html type no longer downloads all the files in the relevant directory. Instead it opens up the html page with broken links. However upon going back into the Galaxy page and clicking download for the second time it reverts back to the old behaviour of downloading the html directory in a zip file, from the second time onwards it maintains this behaviour. Is this how it's intended to work? If so then is there intention to remove the ability to download the html directory? Regards, Shian Su

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Re: [galaxy-dev] Reference Genome in snpEff Tool
by Jennifer Jackson 24 Feb '14

24 Feb '14

Hi Xiaofei, It is best to keep replied on the mailing list. First, confirm that you are running the most current version of the Galaxy distribution. This should be true by default if the installation was just performed. https://wiki.galaxyproject.org/DevNewsBriefs https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10 Since you ran into this issue the first time the server was brought up (or this appears to be the case), you may have run into a characterized issue. On the http://getgalaxy.org page, are two work-arounds for installing eggs in under specific usage circumstances. One is for when running without internet access (probably not the issue). The other is for when using Python 2.7 (my best guess as the problem). Both are included about half-way down the wiki page, toward the end of the 'Start it up' section: https://wiki.galaxyproject.org/Admin/GetGalaxy Please review and see if either if these apply, in particular if the second command ("sh run.sh --reload") solves the issue. Again, please keep feedback on the list, so that the developers can assist us going forward as needed, Jen Galaxy team On 2/24/14 9:51 AM, Wang, Xiaofei wrote: > Dear Jen, > > I really appreciate for your reply! > > We decided to install the local Galaxy for this project. But, when I installed it (I followed the instruction on these 2 links, http://gmod.org/wiki/Galaxy_Tutorial_2013 and https://wiki.galaxyproject.org/Admin/GetGalaxy) I got a problem like this: > > $ sh run.sh > Some eggs are out of date, attempting to fetch... > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 37, in <module> > c.resolve() # Only fetch eggs required by the config > File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve > egg.resolve() > File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources.py", line 576, in resolve > raise DistributionNotFound(req) > pkg_resources.DistributionNotFound: pysam==0.4.2-kanwei-b10f6e722e9a > Fetch failed. > > It seems a problem with the Python '"eggs". But, when I checked the version of Python, it is: > $ python --version > Python 2.7.6 > > Could you help me about what is the problem with the installation? > > Thank you so much! > > Best, > > Xiaofei

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Where to add Account activation
by Danielle Furtado 21 Feb '14

21 Feb '14

I was reading the link: https://wiki.galaxyproject.org/Admin/UserAccounts I wonder where should I add the following line of code in the file universe_wsgi.ini user_activation_on = True I tried adding at the end of the code. I also tried to add in the [app: main] However, it is not functioning. Best Regards, Danielle Furtado.

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With regard to Galaxy tools, a repository should only contain one
by Peter Cock 21 Feb '14

21 Feb '14

Hi all, I've just seen Greg's blog post, "The Galaxy Tool Shed: Best Practices for Populating a Repository" http://gregvonkuster.org/galaxy-tool-shed-best-practices-populating-reposit… One particular point that caught my attention (which I've used as the email title), which seems to signal a move away from "Tool Suites" as a single repository (although they can presumably be emulated by a dummy package defining dependencies on the child tools?). "With regard to Galaxy tools, a repository should only contain one." I look forward to future posts (or emails?) clarifying this... Regards, Peter

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ImportError: No module named json
by Fenglou Mao 20 Feb '14

20 Feb '14

I just upgraded our galaxy server to the latest version, and I got this error in many of the tools: Traceback (most recent call last): File "./scripts/set_metadata.py", line 14, in ? import json ImportError: No module named json And a "find" command below give many a few json eggs, please help. Why Galaxy is not pickung up this json module? (galaxy-env)[galaxy@galaxy galaxy-dist]$ find eggs -name "*json*" eggs/psycopg2-2.5.1_9.2.4_static-py2.6-linux-x86_64-ucs4.egg/psycopg2/_json.py eggs/psycopg2-2.5.1_9.2.4_static-py2.6-linux-x86_64-ucs4.egg/psycopg2/_json.pyc eggs/simplejson-2.1.1-py2.4-linux-x86_64-ucs4.egg eggs/raven-3.1.8-py2.6.egg/raven/utils/json.py eggs/raven-3.1.8-py2.6.egg/raven/utils/json.pyc eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg eggs/boto-2.5.2-py2.6.egg/boto/jsonresponse.py eggs/boto-2.5.2-py2.6.egg/boto/jsonresponse.pyc eggs/boto-2.5.2-py2.6.egg/boto/sqs/jsonmessage.pyc eggs/boto-2.5.2-py2.6.egg/boto/sqs/jsonmessage.py

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