Question: FTP Upload to Galaxy
0
gravatar for rooneyl
2.2 years ago by
rooneyl0
United States
rooneyl0 wrote:

 

Please give me step by step instructions on who to ftp (upload) my sequence files to Galaxy server?  

Thanks,

LeeAnn

 

upload galaxy • 680 views
ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson23k • written 2.2 years ago by rooneyl0

How not who (haha)

 

Apparently I have to use ftp as my files is larger than 2GB

ADD REPLYlink written 2.2 years ago by rooneyl0
0
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Here is the help: https://wiki.galaxyproject.org/Support#Loading_data

Best, Jen, Galaxy team

ADD COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson23k

Thanks Jennifer that was very helpful, I will CyberDuck. Do you know if the file has to be uncompressed first or not? Do I have to specify the path, if not where does the data go? LeeAnn


From: Jennifer Hillman Jackson on Galaxy Biostar [notifications@biostars.org] Sent: Thursday, October 29, 2015 10:20 AM To: LeeAnn Rooney Subject: [galaxy-biostar] A: FTP Upload to Galaxy

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: FTP Upload to Galaxy<http: biostar.usegalaxy.org="" p="" 14830="" #14833="">:

Hello,

Here is the help: https://wiki.galaxyproject.org/Support#Loading_data

Best, Jen, Galaxy team

ADD REPLYlink written 2.2 years ago by rooneyl0

Filezilla is a better choice now, but really you can use whatever FTP client you want, as long as passive FTP is present (or not use a client and just connect on the command-line).

The data goes into a holding area specific to your account. Any files you load will be available under the Upload tool where they can be moved into a history for use with tools.

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson23k

Hi Jennifer, Thanks, that was helpful and I did get my files ftp'ed to Galaxy. I am processing as usual, which involves five simple steps.

1) upload reads 2) convert format from FASTQ to FASTA 3) Clip Adaptor sequence and all sequence 3' of the adaptor on reads 4) upload fasta reference sequence (human CFTR) 5) Align reads to reference sequence using LASTZ (very high stringency, see second screen shot)

So again the LASTZ is hung (gray) waiting to run, see first screen shot. Do you have anyway of moving my jobs up in the queue or checking to be sure that these are indeed going to eventually run? I have 6 total.

Thanks, LeeAnn

P.S. we are also setting up a cloud based Galaxy at OHSU in hopes of expediting this data analysis, but customizing it may take some time...

ADD REPLYlink written 2.2 years ago by rooneyl0

A grey dataset is queued. This occurs when either you have other jobs queued/running that were started before this one, or the Galaxy cluster is simply busy. Give it time as allowing it to execute is the best. If you delete and restart, the job just goes back to the end of the queue. 

https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Jen

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 114 users visited in the last hour