[galaxy-user] Job waiting to RUN

2012-04-13 Thread Ateeq ur Rehman
Dear Administrators Since yesterady my bowtie alignment is waiting to run, message is just, job waiting to run could you plesae see the problem Thank you Ateequr Rehman ___ The Galaxy User list should be used for the discussion of

[galaxy-user] wig to bigwig error

2012-04-13 Thread Michael Sikes
Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I

Re: [galaxy-user] History not accessible

2012-04-13 Thread Jennifer Jackson
Hi Luciano, The '228Gb' number can take some time to update, but this should be be a most few hours, not an entire day. To remove datasets from a history permanently (and remove them from disk) you will need to do two things: 1 - delete by clicking on the X for those datasets 2 - use

Re: [galaxy-user] Job waiting to RUN

2012-04-13 Thread Jennifer Jackson
Hi Ateequr, We can let you know that the public main Galaxy instance is very busy right now and this is the cause for the delay. A cloud instance many be a solution for your or others reading this post. Help to get started is in this wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud Take care,

Re: [galaxy-user] Alignment coordinates

2012-04-13 Thread Jennifer Jackson
Hi Erika, Unfortunately, Galaxy does not have a parser tool to transform clustal datatypes into tab-coordinate based files. Sorry we couldn't help! Best, Jen Galaxy team On 4/12/12 8:07 AM, Erika Kruse wrote: Hello, I imported a sequence alignment file from clustalw. How can I generate a

Re: [galaxy-user] Alignment coordinates

2012-04-13 Thread Ross
Erika, Although Galaxy doesn't have a suitable mapping tool for fasta format sequences, you can use the Galaxy clustalw tool option to output a fasta format file and then upload that fasta file to the ncbi Blast tool at http://blast.ncbi.nlm.nih.gov/Blast.cgi to find where the sequences align -

Re: [galaxy-user] wig to bigwig error

2012-04-13 Thread Jennifer Jackson
Hi Michael, This particular .wig file has a data format problem that is the root cause of the conversion error. Specifically, there is an extra track line in the file. This can be found using unix tools with a grep or in Galaxy with the tool Filter and Sort - Select by matching the pattern

Re: [galaxy-user] Job waiting to RUN

2012-04-13 Thread Wang, Michael
Hi Jen, I am experiencing the same issue (job pending since yesterday) as Ateequr, but not with other tools such as pileup. Are you sure this is due to heavy load, not because of problems with Bowtie tool? It might just take a while for me to figure out how to use your cloud instance. Thanks,

Re: [galaxy-user] FASTQ joiner fails to join PE data.

2012-04-13 Thread Jennifer Jackson
Hello, The FASTQ Joiner tool is currently being updated to work with the newer sequence Id format. The progress of this change can be tracked here: https://bitbucket.org/galaxy/galaxy-central/issue/677/update-joiner-tool-to-work-with-casava-18 Meanwhile, quality filtering can be done on

Re: [galaxy-user] Editing workflows : Server error ?

2012-04-13 Thread Jennifer Jackson
Hi Sandrine, Would you have time to share one of these workflows that produces a Server error, so that we can examine your exact case and determine the root cause of the problems? To do this, on the Your workflows page, use the pull-down menu to select Share or Publish, generate a share