July 2011 - galaxy-dev - lists.galaxyproject.org

Data library fails to display contents
by W. Augustine Dunn III 16 Aug '11

16 Aug '11

I am starting to really get the hang of customizing my new galaxy instance, and please just let me THANK YOU GUYS! However, I am also running into a problem. I am trying to link genome fasta files that i obtained through metazoa.ensembl.org. I created a library called "Genome Sequences" with sub-folders to house them. Everything was going fine until I tried to change the info on a couple so that they were fasta not so other randomly autoassigned type. Now I get this error msg when ever i try to browse ANY of the "Genome Seq" Library: Error attempting to display contents of library (Genome Sequences): 'NoneType' object has no attribute 'dataset'. I am running this instance using a postgresql backend but the default paste web-server since its mostly gonna me me and one or two other lab-mates using it. I can NOT figure out whats up. Relevant excerpt of Server log follows: xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:03 -0700] "GET / HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /root/tool_menu HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /history HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin HTTP/1.1" 200 - "http://vlad.bio.uci.edu:8081/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin/center?webapp=galaxy HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:10 -0700] "GET /library_admin/browse_libraries HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_admin/browse_libraries?f-deleted=False&f-name=All&f-description=All&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=browse&id=9a8774fee61dd122& HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_common/browse_library?sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp=galaxy&id=9a8774fee61dd122&page=1 HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_admin/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%28Genome+Sequences%29%3A+__sq__NoneType__sq__+object+has+no+attribute+__sq__dataset__sq__. HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" Thanks in advance! And thanks for this priceless tool! Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*

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Defining new file formats in Galaxy (for new tool wrappers)
by Peter Cock 15 Aug '11

15 Aug '11

Hi all, Something I've not needed to do until now is define a new file format in Galaxy. I understand the basic principle and defining a subclass in Python... however, how does this work with new tools on the Tool Shed? In particular, if an output format is likely to be used by more than one tool, can we get it added to the Galaxy core? As an example, the basic functionality of the Blast2GO for pipelines tool (b2g4pipe) takes a BLAST XML input file, and gives a tab separated annotation output file. Galaxy already has 'blastxml' and 'tabular' file formats defined, so I didn't need to do anything extra. However, the tool can also take (a directory of) InterProScan XML files as input, so here a new 'interproscanxml' format would useful. Then any wrapper using or producing InterProScan XML could take advantage of this. e.g. Konrad's InterProScan wrapper could then offer the XML output as an option in addition to or instead of the tabular output. Related to this example, why isn't there a generic base class for XML formats in general? https://bitbucket.org/galaxy/galaxy-central/issue/568/missing-xml-datatype-… Regards, Peter

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Catch problems preparing cluster job scripts
by Peter Cock 09 Aug '11

09 Aug '11

Hi all, I've run into some file permissions problems as part of using the same mapped directory on both the Galaxy server and our cluster. In the process I wrote the following patch which fixes the following bug - where Galaxy seems to leave the job in the pending state: galaxy.jobs INFO 2011-07-29 14:06:46,170 job 30 dispatched galaxy.jobs.runners.drmaa ERROR 2011-07-29 14:06:46,582 Uncaught exception queueing job Traceback (most recent call last): File "/data/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 114, in run_next self.queue_job( obj ) File "/data/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 164, in queue_job os.chmod( jt.remoteCommand, 0750 ) OSError: [Errno 1] Operation not permitted: '/data/galaxy/galaxy-central/database/pbs/galaxy_30.sh' The jobs was left stuck in the grey pending state. It looks like this exception should have been caught and the job put into an error state as in this patch: https://bitbucket.org/peterjc/galaxy-central/changeset/c5fa48633c0b This is currently the one and only change on this branch: https://bitbucket.org/peterjc/galaxy-central/src/job_scripts Please could this be reviewed and applied to the trunk. Thanks, Peter

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Request for pulling the updated FASTQ (de-)interlacer tool
by Florent Angly 06 Aug '11

06 Aug '11

Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository: https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent

3 4

BWA wrapper with Illumina-1.3+ FASTQ files
by Assaf Gordon 05 Aug '11

05 Aug '11

Hi, The attached patch enables the BWA wrapper to work with Illumina-1.3+ FASTQ files without Grooming (which goes well with the name of the tool: "Map with BWA for Illumina" ). Actually, Changing the XML and the python code, testing the tool and mapping to the mouse genome all together took less time than grooming one 4.2GB FASTQ file :) Comments are welcomed, -gordon

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scripts/make_egg_packager.py broken
by Sonderegger Bernhard 03 Aug '11

03 Aug '11

Hi all, The scripts/make_egg_packager.py script appears to be broken I get the following message: Traceback (most recent call last): File "scripts/make_egg_packager.py", line 21, in <module> c = Crate() TypeError: __init__() takes at least 2 arguments (1 given) Thanks for any suggestions. B.

2 1

Hidden history item
by Bossers, Alex 03 Aug '11

03 Aug '11

Hi all, by default I let my tools produce ("the old way") a logfile of the console and additional running statistics. This is convenient at tool setup and ocassionally for troubleshooting. Anyway I would like to make the corresponding history item hidden. I tried including hidden="true" in the output tag but that does not make any difference. Is this possible at all or only applicable to running workflows? Any pointers appreciated. Alex

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Workflow Bug?
by John Chilton 03 Aug '11

03 Aug '11

Hello Galaxy Developers, I have a user who noticed a potential bug when extracting workflows from histories on our local Galaxy server. I have recreated the bug on the public Galaxy server with a much smaller history. The history can be found here: http://main.g2.bx.psu.edu/u/jmchilton/h/column-join-workflow-bug Basically when creating workflows from such histories, the second input to "Column Join" never seems to be connected to the previous step the way I would expect it to be. In the workflow editor you can manually create this connection, but it is easy to miss this in a large worfklow and have incomplete results as a consequence. Am I missing something or is this a bug? Thanks for your time, -John

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Does Galaxy have a tool to run R script?
by liu bo 02 Aug '11

02 Aug '11

Dear all, I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help. Thank you, Bo Liu

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approximate line numbers shown in history items can be very imprecise
by Chaolin Zhang 02 Aug '11

02 Aug '11

Hi, I noticed that the current version of galaxy shows approximate number of lines for history items, when it is relatively big. I guess this is due to a consideration of performance, but it is quite annoying, because the exact line numbers provide a very easy way for users to get simple statistics. Sometimes the approximation can be really off. For instance, for one file with > 1 M lines, it shows ~850,000 lines. Any thought? Chaolin

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