[galaxy-user] Galaxy down?
Hi, is there currently a problem with the Galaxy Server? When will it be up again? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Bowtie Job doesn't start
Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] upload of Zea mays genome to galaxy?
Last time I checked there was an up to date zea mays genome already available in galaxy. Am 05.03.2011 21:49, schrieb karlerh...@berkeley.edu: Hello, I'm interested in using the galaxy tools to analyze some transcriptome libraries I made of maize seedlings. Would it be possible to upload the maize reference genome to the galaxy browser? It's available at the following website: http://ftp.maizesequence.org/current/ Hope this can be done, would be really exciting! Thanks, Karl ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Cleaning of fastq files
Hi, is there a way to clean fastq files (filter Poly-A etc.) with Galaxy? Haven't found anything so far. Also if you generally know good tools plz answer. Have seen lots of stuff for fasta and qual files but not for fastq. Thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Text Manipulation
Hi Peter, sounds nice, would be a great feature. For everyone else how is not using a custom server: if you are lucky you can use the trim tool on tabs to solve your problem. If you want to add text to the beginning or end of a column: - Use add column and add the text as a new column - Then use cut to get everything in the right order - finally join the new column with the column you want to add the text to I hope you get what I mean and is helpful to someone Using these tricks I have created a work flow that serves as my custom sam to gff converter. Of course its terribly inefficient, but it gets the job done. thx, Felix On Tue, Feb 22, 2011 at 2:28 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Felix, Text Manipulation - Convert delimiters to TAB could split one field into more than one, but the delimiter has to be in the list (@ is not). Text Manipulation - Cut columns from a table is similar, but it will not split on a @ either. Text Manipulation - Trim leading or trailing characters could be use for this specific case, since you can trim off the end of a column based on a position (but again, not a specified delimiter). To prep for an entire genome, you would need to break up the starting query so that the chromosome name lengths in any derivative queries are of a consistent length, then merge back together. Perhaps the @ was just an example and one of these tools will work for you. If you are customizing, additions to the Tool Shed that expand the native tools are always welcome! http://community.g2.bx.psu.edu I've been planning to write a Galaxy tool to split a column on a given delimiter (e.g. @ for this example, or | for NCBI style identifiers), which would solve this use case nicely. I haven't done it yet though - so if anyone else wants to write such a tool first, please go ahead. Specifically I would be aiming to expose the Python split and rsplit string method functionality, so the user would have to specify the number of splits (or perhaps more intuitively the number of columns to make) and if it should start on the left (default) or on the right. Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Group and hide steps in history/workflow
Hi, it would be really nice if I could take a work flow and save it as a tool. This way one could easily build custom text-manipulation tools from already existing text tools. I already have a work flow that does a conversion job. But it has lots of of steps that make my histories quite messy when I apply it. Is there a way to condense the steps in the history view, so you can only see the name of a work flow and not all the separate steps? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] SAM to GFF ?
Hi, is there an easy way to use Galaxy to convert SAM to GFF? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] GeneTrack Server Error
Hi, I am trying to view Converted Interval Data in GeneTrack, but all I get is Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Mapping does not start
Hi, I am trying to map sequences with Bowtie. Have been waiting for a few hours now but it still says Job is waiting to run. A few days ago I didn't have this problem and the job started immediately. My guess is that the jobs are still stuck in a queue? How can I tell when the jobs will approximately start running? Is there a way to view the queue position? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
