Question: Freeing usage space in Galaxy
0
gravatar for mariel.voutounou
2.9 years ago by
United States
mariel.voutounou0 wrote:

Hello, 

I have reached a 94% usage space and I would to know how I could free up some space.

I have already permanently deleted some past data - but that did not increase the current space.

 

Kind Regards,

 

Mariel 

usage space • 1.0k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by mariel.voutounou0
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

I believe that I found your account and ran a recalculation on the disc usage. No change. Are you certain that the data has been permanently deleted? This is how to check: Delete_vs_Delete_Permanently

Let us know how this works. Best, Jen, Galaxy team

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k

Hello Jen,

Thank you for the swift response. in all cases that i have deleted data, I chose the permanent deletion. I just gave it another go - i permanently deleted a data set 111 GB big, but again no change - So indeed it doesn’t seem to delete them (even if I choose the permanent deletion and they get removed from the list).

Is there any way to find the deleted items and try to permanently delete them again?

Kind Regards,

Mariel

ADD REPLYlink written 2.9 years ago by mariel.voutounou0

Hello,

I both looked at your account and ran the process to recalculate disk usage. All seems to be correct now. At about 50% usage. Different than earlier - guessing that the correct data is now permanently deleted. Instructions with a video were in the link I sent you, perhaps that is what helped? If so, am glad! Take care, Jen

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k
0
gravatar for mariel.voutounou
2.8 years ago by
United States
mariel.voutounou0 wrote:

Dear Jennifer,

I have another question in regards to Galaxy that you might be able to help me with.

We usually get our Galaxy results in FPKM for each gene. What I would like to know is, if it is possible to also get the counts for each gene and if there is an easy way to do that.

Thank you in advance,

Kind Regards,

Mariel

ADD COMMENTlink written 2.8 years ago by mariel.voutounou0

Mariel,

Next time, would you please post new questions in a distinct new post? This helps others to find replies. And if you need more help for this one, definitely start a new post thread (you can include a link to this one, for context).

But to get you a quick reply, I can let you know that the option "Include Count Based output files" on the Cuffdiff tool form is most likely what you are looking for. Check the tool's manual to understand the contents of these output files to see if they are a match for what you expect.

Just to help you to find answers like this quickly, please know that links to documentation for 3rd party tools is almost always on tool forms, in the "help" section found under the run-time options. The Cuffdiff form includes this. If for some reason you are using a tool without that sort of link, "Options -> See in Tool Shed" will bring up the tool wrapper details, including the underlying tool version, and a google with that information will take you to where you can find usage details. But if ever you can't find what you need to know for some reason, please know we'll do our best to you here, too!

Jen, Galaxy team

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson25k

Jen,

Thanks for the reply& suggestions. I will give it a go.

Mariel

ADD REPLYlink written 2.8 years ago by mariel.voutounou0

Dear Jen,

I was able to find the counts on the Cuffdiff tool form -

My question now is what does the decimal point stand for?

For example:

Gene WT Test F2rl2 5566.54 10305.4

Kind Regards,

Mariel

Mariel Voutounou, Ph.D. Burke Medical Research Institute, Department of Neurology & Neuroscience, Weill Medical College of Cornell University, 785 Mamaroneck Ave, White Plains, NY10605<x-apple-data-detectors: 0="" 0=""> Tel:(914) 426-3682<tel:(914)%20426-3682>

ADD REPLYlink written 2.8 years ago by mariel.voutounou0

Begin forwarded message:

From: Mariel Voutounou <mav3001@med.cornell.edu<mailto:mav3001@med.cornell.edu>> Subject: Galaxy Counts - decimals Date: August 31, 2015 at 10:27:45 AM EDT To: galaxystar+3e7c65fc+code@biostars.io<mailto:galaxystar+3e7c65fc+code@biostars.io>

Dear Jen,

Thank you for your help in regards to finding the Counts in Galaxy. I am resending my previous email in case you did not receive it the first time around.

In regards to the counts, I would also like to know what does the decimal point stand for?

For example we got:

Gene WT Test F2rl2 5566.54 10305.4

Please get back to us to your earliest convenience as we need to use the count data, and are on a deadline!

Kind Regards,

Mariel

Mariel Voutounou, Ph.D. Burke Medical Research Institute, Department of Neurology & Neuroscience, Weill Medical College of Cornell University, 785 Mamaroneck Ave, White Plains, NY10605<x-apple-data-detectors: 0="" 0=""> Tel:(914) 426-3682<tel:(914)%20426-3682>

ADD REPLYlink written 2.8 years ago by mariel.voutounou0
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