I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie, SAMtools, and Tophat all run fine with my small subset of paired-end Illumina reads. Unfortunately, it seems to only partially work when I run Cufflinks v2.0.2. Three entires in my history appear (gene expression, transcript expression, and assembled transcripts) containing reasonable output. Each of these entries is highlighted red, though without the red circle with an X. The box contains the message: An error occurred running this job: cufflinks v2.0.2 cufflinks -q --no-update-check -l 300000 -F 0.100000 -j 0.150000 -p 4 cp: cannot stat ` /home/galaxy/galaxy-dist/database/job_working_directory/000/20/global_model.txt': No such file or directory What is this global_model.txt file and why might it be missing/have failed? (sorry about the repost... original got embedded in an unrelated thread)
The Cufflinks wrapper doesn't support v2.0 or greater yet. Please use v1.3.0 for now. We expect to update the Cufflinks wrapper to support v2.0+ in the next couple weeks. Best, J. On Sep 25, 2012, at 5:34 PM, wormbuff wrote:
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie, SAMtools, and Tophat all run fine with my small subset of paired-end Illumina reads. Unfortunately, it seems to only partially work when I run Cufflinks v2.0.2.
Three entires in my history appear (gene expression, transcript expression, and assembled transcripts) containing reasonable output. Each of these entries is highlighted red, though without the red circle with an X. The box contains the message:
An error occurred running this job: cufflinks v2.0.2 cufflinks -q --no-update-check -l 300000 -F 0.100000 -j 0.150000 -p 4 cp: cannot stat ` /home/galaxy/galaxy-dist/database/job_working_directory/000/20/global_model.txt': No such file or directory
What is this global_model.txt file and why might it be missing/have failed?
(sorry about the repost... original got embedded in an unrelated thread) ___________________________________________________________ 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:
participants (2)
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Jeremy Goecks -
wormbuff