[galaxy-dev] How to get a local file into the dataset window/browser?
I have BAM files sitting in database/files that I want to automatically (ie: not through the Upload File tool) import/display via a tool/script/process other in the dataset pane (sorry, not sure of proper terminology, but the History/right side pane). How do I locate these files and display/load them via a tool or script? Is there a script or particular system call, a change to data_source.py or anything that will make them show up? Thanks so much, Brian ___ 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/
[galaxy-dev] Custom Get Data page doesn't recognize completion of large file downloads
I have a custom module/page created to get data from some SOAP-based web services. I haven't determined the threshold yet, but for small BAM files, Galaxy behaves just fine. However, when I get large BAM files (I've had the same results with 10gig and 40gig files), Galaxy doesn't recognize when the download is complete. I can look in the /database/files/000 directory and see the download is complete (md5sum confirms it), but Galaxy just keeps on saying Job is currently running. It takes a Galaxy reboot for it to recognize the complete download. Any ideas on how to fix this? Thanks -Brian ___ 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/
[galaxy-dev] Error with large BAM files?
Hello, I'm very new to Galaxy development. What we've got is a tool we've created that will use our own API/web services in order to use BAM files in our database as the data source in Galaxy. I got it to work on a very tiny BAM file, but now that that is working, I tried it on a larger one and am seeing the following error: An error occurred running this job: Unable to fetch https://[address to method calling web service]: 'ascii' codec can't decode byte 0xc2 in position 25686: ordinal not in range(128) As far as I can tell from Google, it appears this error has to do with python expecting ascii, but I'm calling Galaxy with the following code: String MimeType = application/octet-stream; BufferedOutputStream out = new BufferedOutputStream(response.getOutputStream()); byte[] result = [call to my web service]; response.setContentType(MimeType); response.setHeader(Content-Disposition,attachment;filename=GalaxyResponse); out.write(result, 0, result.length); Is there anything wrong with this? Or is there some other code I might need to modify, such as in data_source.py? Any help is appreciated, thanks! Brian Luerman Intrepid Bioinformatics (502) 212-2699 http://intrepidbio.com/ ___ 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/
