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

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 l

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

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 each

Re: [galaxy-user] Help!! Uploading with FTP

Hello Jiwen, You would have to compare this with your regular transfer speed, but this does seem to be on the low side. Galaxy being busy could have some influence on transfers, but not at the level that you are reporting. I just ran a test using FileZilla and transferred a 56M file in a litt

[galaxy-user] Help!! Uploading with FTP

Hi, I am uploading files to Galaxy via FTP. The speed is only 30kb/sec. Is there something wrong with my operation? or is this just normal due to Galaxy's work load? Looking forward to your answers. Thanks Jiwen ___ The Galaxy User list sh

Re: [galaxy-user] Job waiting to RUN

Hi Michael, Yes, we are certain that Galaxy is processing jobs and is experiencing a heavy user load. The variable job working time is due to the type of job and which of our clusters it runs on. We have substantial resources dedicated to the NGS mapping jobs, and job quotas help to ensure t

Re: [galaxy-user] Job waiting to RUN

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, Mi

[galaxy-user] Editing workflows : Server error ?

Dear all, I didn't use Galaxy for some weeks now. When I tried to edit some of my workflows today I received an error message "Server error" instead. Is there any problem with the workflow editor or to edit big workflows (>40 steps) recently ? It seems that I can only edit workflows with a limited

Re: [galaxy-user] wig to bigwig error

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] Alignment coordinates

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 - bl

Re: [galaxy-user] Alignment coordinates

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] Job waiting to RUN

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, J

Re: [galaxy-user] History not accessible

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 'Optio

[galaxy-user] wig to bigwig error

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 tr

[galaxy-user] History not accessible

Hi, After I uploaded a couple files yesterday, I hit the storage limit (250Gb), then I deleted 3 datasets from my history and now I can't see anything in that history. It still says that I am using 228Gb, but I can only access one history with ~98Gb. I try to use show deleted datasets and it still

[galaxy-user] Job waiting to RUN

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 G