February 2013 - galaxy-user - lists.galaxyproject.org

Error using Trackster
by Kilaru, Varun 01 Feb '13

01 Feb '13

Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error: hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate? Thanks, Varun ________________________________ 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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Error using trackster
by Kilaru, Varun 01 Feb '13

01 Feb '13

Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error: ________________________________ 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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February 2013 Galaxy Update
by Dave Clements 01 Feb '13

01 Feb '13

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error message running Cufflinks on local galaxy
by Davide Degli Esposti 01 Feb '13

01 Feb '13

Dear Jen, I have downloaded Galaxy on my computer. When trying to run cufflinks locally I have this error message: 8: Cufflinks on data 3 and data 2: gene expression error An error occurred running this job:Could not determine Cufflinks version cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.150000 -p 4 -G /Users/davidedegliesposti/galaxy-dist/database/files/000/dataset_2.dat -N Error running cufflinks. return code = 127 /bin/sh: cufflinks: command May this be due to an error of installation? Thank you for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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error running cufflinks
by Davide Degli Esposti 01 Feb '13

01 Feb '13

Dear Jen, after a couple of days of running cufflinks on a sam file (data 9) with an annotated reference in gtf (data 28), I have this message in return that I am not able to decode: 32: Cufflinks on data 9 and data 28: total map mass error An error occurred running this job:cufflinks v2.0.2 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.150000 -p 8 -G /galaxy/main_pool/pool6/files/005/663/dataset_5663874.dat -u -N -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. return code = 1 cufflinks: /lib64/lib Thank you for you help Best regards Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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gather results from multiple histories
by mark.rose＠syngenta.com 01 Feb '13

01 Feb '13

Hi All Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Re: [galaxy-user] [galaxy-dev] extract DNA sequences
by Jeremy Goecks 01 Feb '13

01 Feb '13

Hello, > However, this is not working here. Can you be more specific about what's not working? If the tool failed, please feel free to report the bug using the "bug" icon. > How > do I specify that the strands I am extracting are in the fasta file in my account in Galaxy? GFF requires a strand column, and the tool will automatically use this data to extract sequence data. > Should I be using another tool, please? This is the correct tool. Finally, questions about using Galaxy and its tools are best directed to the galaxy-user mailing list, so I've moved your question to that list. Best, J.

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