Some of the NGS tools like fastx_quality_stats and fastq_quality_boxplot_graph.sh are not available on my local Galaxy install, while others, like the fastq groomer, are. An example error message is:
"An error occurred running this job: /bin/sh: fastx_quality_stats: command not found"
Two questions:
1) Why are these tools not available with the standard install while being listed in the tools list?
2) How do I go about installing them?
Thanks,
Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629
Dean:
These two tools require fastx library that can be obtained here:
http://hannonlab.cshl.edu/fastx_toolkit/
Thanks for using galaxy!
anton galaxy team
On Nov 30, 2009, at 10:46 AM, Dean Snyder wrote:
Some of the NGS tools like fastx_quality_stats and fastq_quality_boxplot_graph.sh are not available on my local Galaxy install, while others, like the fastq groomer, are. An example error message is:
"An error occurred running this job: /bin/sh: fastx_quality_stats: command not found"
Two questions:
- Why are these tools not available with the standard install while
being listed in the tools list?
- How do I go about installing them?
Thanks,
Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629
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Dean Snyder