Hi, I just notice that NGS FASTQ Trimmerhttps://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_trimmer%2Ffastq_trimmer%2F1.0.0by column can't detect the fastq file I loaded. Anyone knows why. thanks a lot.

On Fri, Jan 24, 2014 at 11:00 AM, galaxy-user-request@lists.bx.psu.eduwrote:

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Today's Topics:

1. Re: Creating a Trackster visualisation from a reference in your history (Jeremy Goecks)

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Message: 1 Date: Thu, 23 Jan 2014 15:49:44 -0500 From: Jeremy Goecks jgoecks@email.gwu.edu To: graham etherington (TSL) graham.etherington@sainsbury-laboratory.ac.uk Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Creating a Trackster visualisation from a reference in your history Message-ID: C3382F38-D243-4979-B6A7-BA13EF161EE5@email.gwu.edu Content-Type: text/plain; charset="windows-1252"

...

Is it possible to create a custom build and use it to view a SAM file

without adding the .len and .2bit files in to the Galaxy file system as an administrator?

Yes, it definitely is.

...

If so, what am I doing wrong?

This is a Galaxy bug which has been fixed in this commit:

https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd231516...

We have a release coming up, so this fix will be included in the release and will make it to our public server soon. In the meantime, note that you can use the genome fasta file rather than the len file to create a custom build and everything should work.

Thanks, J.