how to uncompress fastq.gz automatically in galaxy

Question: how to uncompress fastq.gz automatically in galaxy

2.3 years ago by

yychangsd • 30

yychangsd • 30 wrote:

Hi, I set up a local galaxy server.

i'd like to upload the .fastq.gz file and format it to fastq file.

I know it works good in usegalaxy.org

But it does not work and shows

The uploaded binary file contains inappropriate content.

So would you please tell me how to uncompress the fastq.gz files automatically?

I'm a newbie to it and any help would be greatly appreciated...

galaxy • 1.2k views

ADD COMMENT • link •

written 2.3 years ago by yychangsd • 30

Does the same file load fine on usegalaxy.org? What version of Galaxy are you using?

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

Yes, it is exactly the same file loaded on usegalaxy.org My version is 0079d3c5a85d (release_16.01) latest_16.01/v16.01

ADD REPLY • link written 2.3 years ago by yychangsd • 30

Out of curiosity: are you using the BitBucket repository?

Could you please checkout the release_16.04 branch (https://github.com/galaxyproject/galaxy/tree/release_16.04), start Galaxy and see if the upload works for you? Because it does work fine for me.

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

Would you please tell me how to update the release_16.04?

I used hg clone to install galaxy-dist other than git clone to install galaxy.

ADD REPLY • link written 2.3 years ago by yychangsd • 30

Depending on how much data you have in your Galaxy you can either create fresh new instance:

$ git clone https://github.com/galaxyproject/galaxy/
$ cd galaxy
$ git checkout -b release_16.07 origin/release_16.07

or convert your bitbucket repository to github repository using the process described at the bottom of this page: https://wiki.galaxyproject.org/Develop/SourceCode

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

Thanks for your comments. It works out for me if I set up a new instance from my laptop.

But when I set up a new instance from amazon cloud, it seems still not working for me.

The difference between my laptop and amazon cloud (I think) is mac and linux.

So do you have some experience about it?

Thanks.....

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by yychangsd • 30

How do you setup an instance on Amazon? Are you using Cloudman? (https://launch.usegalaxy.org)

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

No, I am not. I use starcluster to prepare a linux cluster from amazon cloud, and then install galaxy in the linux cluster.

I also check the link you sent and found that the latest version from cloudman is 16.04 which is the same version I installed now.

One more question about cloud man. Can I modify the galaxy server from cloud man, such as adding or deleting some tools?

Thanks~~

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by yychangsd • 30

You can control various properties like the number and size of the compute nodes Galaxy uses through Cloudman. The installation of tools is done via Galaxy's interface that Cloudman exposes.

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by Martin Čech ♦♦ 4.9k

Thanks !! I installed one! Is it possible to add or delete some sections? It contains quite a lot sections and I'd like to delete some of them and also want to add my own sections. I did the same thing as before but it seems does not work. Any ideas? Thanks!!

ADD REPLY • link written 2.3 years ago by yychangsd • 30

You can create sections at the tool installation time. You can hide sections by removing all the tools that are in it from the tool configuration - for the tools included with Galaxy this is in tool_conf.xml

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

I edited tool_conf.xml but it is still the same. Should I restart the galaxy? How can I do it? Thanks~~

ADD REPLY • link written 2.3 years ago by yychangsd • 30

At this point I will send you to read the documentation at https://wiki.galaxyproject.org/Admin/GetGalaxy (and other linked wikipages) since I cannot guide you during every step you take. Please use the resources we have written specifically for this purpose.

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

Similar posts • Search »