just few questions about cuffdiff if anyone can answer:
1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files
2.what to use as input: cufflinks, cuffcompare or cuffmerge?
Thanks a lot!
I deleted several jobs from my history (and purged history as well), however the used space on history hasn't changed.
What is the limit of Gb that can e stored?Can this be updated when files are deleted permanently?
We are pleased to announce a new facility in Galaxy for sharing and publishing Galaxy workflows via the myExperiment social website, which is the leading social website for scientific workflow sharing. myExperiment can now be accessed easily while you're using the Galaxy servers - you can export your workflows to myExperiment to store and share them, and import Galaxy workflows from myExperiment. This means you can:
- Share Galaxy workflows in a controlled way (e.g. within a project), publish them with a stable myExperiment reference for your papers (which is linked-data compatible), and use myExperiment's discovery facilities to find more Galaxy workflows as content grows.
- Use the social website features directly to document, tag and discuss workflows, add licensing, credit and attribution, and to bundle your Galaxy workflows with associated data, documents, presentations etc into myExperiment "packs" for ease of reuse and preservation.
- Benefit from a central workflow website with a broad community, which means you can manage workflows for multiple Galaxy installations, attract visitors to your workflows and research, and network with others.
Instructions are below and in more detail on http://wiki.myexperiment.org/index.php/Galaxy_Help This new facility is brought to you by a myExperiment-Galaxy collaboration and will increase in value as more Galaxy workflows are uploaded so we encourage you to do so - we hope you find it useful and we welcome feedback (contact details are on the help page).
1. When using Galaxy you can import Galaxy workflows from myExperiment by choosing "Upload or import workflow" in Galaxy's workflow menu, then the new "Visit myExperiment" link at the bottom of the page. Within the myExperiment interface you can then view a Galaxy workflow and select "Import this workflow into Galaxy". Some Galaxy tutorial workflows are currently available to help you try this out.
2. To export Galaxy workflows to myExperiment you'll first need a myExperiment username and password, then you'll be able to upload Galaxy workflows and also make them visible to others if you wish. To create a username and password go to http://www.myexperiment.org/ and register. Having a username and password enables you to benefit from all the features of the site.
3. To export a Galaxy workflow to myExperiment select "Download or Export" from Galaxy's workflow menu, enter your myExperiment username and password in the "Export to myExperiment" section and click the "Export" button. Exported workflows are set to be "Private" by default but you can make them visible publicly or to friends, groups etc by clicking on "Click here to view the workflow on myExperiment" and changing the Sharing settings.
4. Visit http://www.myexperiment.org/ at any time to change settings, add further description, tags, license etc, and to create "packs". You can also create and administer groups, link up with friends and network with other workflow users.
Is there a way to generate a pile-up from a BAM file in SAMtools without
including spliced (intronic) regions? Alternatively, is there a way to
split spliced reads in a BAM file?
Thanks in advance!
I want to use Galaxy today but I can't. Galaxy told me that all my account has been marked deleted and I need to contact to Galaxy administrator to restore my accounts.
Could you restore my accounts because I have been started some huge calculus and very important.
Thank's of everything.
I am trying to use LEfSe but keep getting the same error. My data loads
fine, but then I cannot get results from 'Plot LEfSe Results'. I then try
to report the error, but it consistently tells me 'Mail is not configured
for this Galaxy instance". So I don't think my error reports are working.
An error occurred running this job:*Traceback (most recent call last):
File "/usr/local/galaxy-dist/tools/lefse/plot_res.py", line 151, in <module>
else: plot_histo_hor(params['output_file'],params,data,len(data['cls']) ==
File "/usr/local/galaxy-dist/tools/lefse/plot_res.py", li*
Robert Quinn, Ph.D
CFRI Postdoctoral Fellow
NLS 301, 5500 Campanile Dr,
San Diego State University
San Diego, CA, 92182
When using the gene BED to codon BED tool, I noticed that it is not
accurately reporting the codons that make up a gene. For example, some of
the codon are missing (particularly ones that span exon-exon junctions.
Also, when changing reading frame from one exon to the next, the codons are
not read appropriately and the reading frame appears to be decided
arbitrarily. Is this a serious known flaw with the tool or am I missing
Also, is there a version of aaChanges tool that can be used with any genome
(not just human genome?).