[galaxy-dev] Error for draw quality score boxplot

Hi, I have installed the local galaxy and tried to run draw quality score boxplot. It showed the error message: Could not find/open font when opening font arial, using internal non-scalable font Could you please tell me how to fix it ? Thanks, Jianpeng

[galaxy-dev] Error for FASTQ Trimmer by column.

Hi , I have installed our local galaxy and I am trying to run FASTQ Trimmer by column, but I got the error message below: Traceback (most recent call last): File /data/home/galaxy/galaxy-dist/tools/fastq/fastq_trimmer.py, line 41, in if __name__ == __main__: main() File

[galaxy-dev] No Visualization on local galaxy

Hi, I have installed our local galaxy. However, I can not find the Visualization menu on the top of the window. Do you know why ? How to make it show up ? Thanks, Jianpeng This e-mail message (including any attachments) is for the sole use of the

[galaxy-dev] how to configure maximum concurrent jobs for local galaxy

Hi, I have installed our local galaxy. I tried to do some analysis on our local galaxy. However, it seems that I can only run 5 jobs at the same time. When I submitted the 6th jobs, it was in queue until other jobs finished. \ Can you please tell me how to increase the maximum concurrent jobs

[galaxy-dev] Fastq quality score format

Hi, I have installed the local galaxy. In galaxy, I noticed that the quality score of fastq datasets have to be converted to sanger format before mapping with bowtie etc. But I did not find that the mapping tools (e.g. bowtie) require the quality score of fastq datasets must be sanger format.

[galaxy-dev] Output files from Galaxy

Hi, I have installed the local galaxy. I am trying to run some programs. I have a question now: If I run a program and the output file will be in the history. If I want to do something with the output file, it looks like I have to download it at first. Is there a way to do something with the

[galaxy-dev] Data library

Hi, I have installed the local galaxy. And I have tried to use the data library to upload some CEL datasets. However, it occurred an error when I use data library to add datasets. It showed: Miscellaneous information: The uploaded binary file contains inappropriate content error Do you know

[galaxy-dev] Cuffdiff output

Hi, I have ran Cuffdiff and got output files: transcript differential expression testing, gene differential expression testing. Could you please tell me how to get the significant differential expression gene and transcript ? Thanks, This e-mail message

[galaxy-dev] bowtie -X

Hi, I noticed that there is a parameter: Maximum insert size for valid paired-end alignments (-X) for bowtie on Galaxy. The default value on Galaxy is -X 1000. I was wondering if this is the default value we should use ? Or we need to change it to another value ? Thanks a lot. Jianpeng

[galaxy-dev] disk space for local galaxy

Hi, I have installed the local galaxy. I deleted a few histories in order to get some disk space. However, the disk space did not change after the deletion of the histories. Do you why ? How can I get some disk space by deleting histories ? Thanks, This