[galaxy-user] Downloading large files from galaxy
Hi, I seem to be having problems downloading large files from galaxy - the request times out at about 1GB and I'm downloading 2-3GB. Am I doing something wrong? David ___ 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] Downloading large files from galaxy
Hi David, It sounds like the browser is timing out during the download. If possible for you to do, a good alternative is get the data through a unix shell using wget or curl. The link to download can be obtained by right clicking the floppy disk icon inside a history item and choosing Copy Link Address. Once you have the link: % wget 'link' or % curl -O 'link' The quotes aren't strictly necessary but will prevent the shell from evaluating the '?' character in the link. Best, Jen Galaxy team On 9/13/11 5:06 AM, David Matthews wrote: Hi, I seem to be having problems downloading large files from galaxy - the request times out at about 1GB and I'm downloading 2-3GB. Am I doing something wrong? David ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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] Help with sam to bam
Hi, I was wondering if someone could help me with an error message I'm getting after performing a sam to bam conversion in galaxy. I've used Bowtie to map sequence reads to a custom fasta file corresponding to one chromosome in my organism. The mapping seems to work fine, but when I attempt a sam to bam conversion, I receive the folowing error message: An error occurred running this job: Samtools Version: 0.1.12 (r862) Error creating indexes from reference (/galaxy/main_database/files/002/977/dataset_2977193.dat), [fai_build_core] line length exceeds 65535 in sequence 'LGVII'. Segmentation fault Any help would be appreciated. Thanks, Zack ___ 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] BFAST for SOLID paired end reads
I am new to RNA-Seq and trying to map ABI SOLID paired-end reads. I've read that BFAST + BWA is a good program for this. I have found BFAST on the galaxy test site. Is it possible to map paired end reads using the BFAST version there? Could someone help me with this workflow? Thanks very much in advance. ___ 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] Trinity
I want to run Trinity on the test instance of Galaxy, but there seems to be a problem. The analysis complete very quickly and I've got no assembled transcripts. In the log file created by Trinity, there is one line: /var/spool/torque/mom_priv/jobs/1204985.thumper.g2.bx.psu.edu.SC: 11: Trinity.pl: not found Any idea? David ___ 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] MACs
Does anyone have advice on how to set the fdr threshold when using MACs in galaxy? Conversely, is there a way to learn what the fdr is for each peak that is called? ___ 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/
