fastx_toolkit not recognizing fastq files
Hello, I've installed Galaxy on two separate machines. None of the fastx tools recognize my fastq files. They are not appearing in the drop down list on Galaxy for input options. I'm getting the same behavior on both machines. I've used the tool_shed to install fastx on one machine and I've done it manually on the other. fastx_tools work perfectly from the command line. Cheers Ian
If you look at the attribute details for one of your fastq files, what does Galaxy say the filetype is? You most likely need to flip it from 'fastq' to 'fastqsanger' so Galaxy will know how to handle the file, it doesn't automatically detect this. -Dannon On Mon, Oct 7, 2013 at 10:38 AM, UMD Bioinformatics < bioinformatics.umd@gmail.com> wrote:
Hello, I've installed Galaxy on two separate machines. None of the fastx tools recognize my fastq files. They are not appearing in the drop down list on Galaxy for input options. I'm getting the same behavior on both machines. I've used the tool_shed to install fastx on one machine and I've done it manually on the other.
fastx_tools work perfectly from the command line.
Cheers Ian ___________________________________________________________ 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/
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Thanks Dannon! That was the fix. It's odd that it isn't part of the auto detect feature. -Ian On Oct 7, 2013, at 10:46 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
If you look at the attribute details for one of your fastq files, what does Galaxy say the filetype is? You most likely need to flip it from 'fastq' to 'fastqsanger' so Galaxy will know how to handle the file, it doesn't automatically detect this.
-Dannon
On Mon, Oct 7, 2013 at 10:38 AM, UMD Bioinformatics <bioinformatics.umd@gmail.com> wrote: Hello, I've installed Galaxy on two separate machines. None of the fastx tools recognize my fastq files. They are not appearing in the drop down list on Galaxy for input options. I'm getting the same behavior on both machines. I've used the tool_shed to install fastx on one machine and I've done it manually on the other.
fastx_tools work perfectly from the command line.
Cheers Ian ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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Dannon Baker -
UMD Bioinformatics