March 2012 - galaxy-dev - lists.galaxyproject.org

Setting genome build on datasets transferred from sample tracking external service
by Leandro Hermida 30 Mar '12

30 Mar '12

Dear Galaxy Dev, Is there a way to set the genome build metadata on datasets transferred from an external service in the sample tracking system? -Leandro

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bug previewing data
by Bartlett G Ailey 30 Mar '12

30 Mar '12

Hi, This is a new galaxy install and my initial test was downloading exon data from UCSC Main. The data failed to preview, I tried various alternatives and it seems to be related to the size of the data. Exon data from Chromosome 1-15 is displayed correctly while Chromosome 16-22 does not display any data at all. When I varied the types of downloads I noticed that files greater than 1MB were displayed while those less were not. There is text on the preview screen stating that only the first 1MB of data will be displayed if it is greater than 1 MB. The small window in the History pane does display correctly. This is a strange error for a configuration mistake but I know the public server does not have the error so I have made a mistake somewhere. The log file does not display any errors though. Any suggestions on a solution or how to get more information on the error? Bart.

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Text field parameter with preset values
by Yuri D'Elia 30 Mar '12

30 Mar '12

When writing a custom tool's xml, is it possible to have a text field with a drop-down list of preset values? To make this more clear, I would like to have the same effect of the "File Format:" text box of the "Upload File" tool, but allow the user to enter any arbitrary text. It seems that <param type="select"> only generates a drop-down list that cannot be overridden. <param type="text"> instead does not allow to pre-set some common values. Any suggestion? Thanks

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how to configure maximum concurrent jobs for local galaxy
by Xu, Jianpeng 30 Mar '12

30 Mar '12

Hi, I have installed our local galaxy. I tried to do some analysis on our local galaxy. However, it seems that I can only run 5 jobs at the same time. When I submitted the 6th jobs, it was in queue until other jobs finished. \ Can you please tell me how to increase the maximum concurrent jobs ? Thanks, Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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What AWS regions is Galaxy Cloud supported in ?
by Greg Edwards 29 Mar '12

29 Mar '12

Hi, What AWS regions is Galaxy Cloud supported in at present ? I believe it's US East (Virginia) and Singapore. Thanks, Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

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Error for FASTQ Trimmer by column.
by Xu, Jianpeng 29 Mar '12

29 Mar '12

Hi , I have installed our local galaxy and I am trying to run FASTQ Trimmer by column, but I got the error message below: Traceback (most recent call last): File "/data/home/galaxy/galaxy-dist/tools/fastq/fastq_trimmer.py", line 41, in if __name__ == "__main__": main() File "/data/home/galaxy/galaxy-dist/tools/fastq/fastq_trimmer.py", line 17, in main for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): File "/data/home/galaxy/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 456, in __iter__ yield self.next() File "/data/home/galaxy/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 452, in next rval.assert_sequence_quality_lengths() File "/data/home/galaxy/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 209, in assert_sequence_quality_lengths assert qual_len + 1 == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) AssertionError: Invalid FASTQ file: quality score length (100) does not match sequence length (100 with adapter base) What is the problem with it ? Thanks a lot. Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Re: [galaxy-dev] Error when installing galaxy - Email found in subject
by Jemma Wu 29 Mar '12

29 Mar '12

Hi Dave, Thank you very much for your reply! The problem has been fixed after I installed python-boto. Regards, Jemma -----Original Message----- From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Emil Bouvier Sent: Wednesday, 28 March 2012 11:55 PM To: Jemma Wu Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] Error when installing galaxy - Email found in subject Jemma, It looks like the boto package is not installed on your system. Try: sudo apt-get install python-boto Dave B. On 3/18/12 8:19 PM, Jemma Wu wrote: > Dear Galaxy developers, > > This is the first time that I installed Galaxy on a Debian Lenny 64 > bit server. I got an error of "ImportError: No module named boto" when > I ran %sh run.sh. Please see the error message of the installation output below: > > File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, > in app_factory > > add_ui_controllers( webapp, app ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, > in add_ui_controllers > > module = __import__( module_name ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py", > line 9, in <module> > > import boto > > ImportError: No module named boto > > Does anyone know how to fix this error? Thanks in advance! > > Regards, > > Jemma > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you.

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Proteomics category on main toolshed?
by Ira Cooke 29 Mar '12

29 Mar '12

Dear list, I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category. Would it be possible to add a category called Proteomics? Thanks Ira

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No Visualization on local galaxy
by Xu, Jianpeng 29 Mar '12

29 Mar '12

Hi, I have installed our local galaxy. However, I can not find the Visualization menu on the top of the window. Do you know why ? How to make it show up ? Thanks, Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Does Any Galaxy Format Converter Support Parallel Format Conversion?
by yi wang 29 Mar '12

29 Mar '12

Hi, Galaxy provides a couple of data format converters, but do they support format conversion in parallel? Where can I find the source code for these converters? Thanks, Yi Wang

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