Re: [galaxy-dev] Question about compressed files

2012-07-04 Thread Björn Grüning
Hi Ciara, Galaxy supports compressed files like gz [1] by default. Keep in mind that large files like yours are not guaranteed to upload properly, please use other techniques to get your data in galaxy. For example with FTP: http://wiki.g2.bx.psu.edu/FTPUpload Hope that helps, Bjoern [1]

Re: [galaxy-dev] Question about compressed files

2012-07-04 Thread Ciara Ledero
Thanks for the quick reply. I've already checked how to configure our Galaxy instance for FTP upload, but due to security reasons, I cannot use that option. I read the wiki for Data Libraries and found that uploading via filesystem path can be used for putting files with size greater than 2GB in

[galaxy-dev] Byte-range support for IGV ?

2012-07-04 Thread Chebbi Mohamed Amine
HELLO ! I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message : HTTP and FTP access to BAM files require byte-range support Has anyone encountred the same probleme?

Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch

2012-07-04 Thread Bernd Jagla
Dannon Baker dannonbaker@... writes: Hi Dave, Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single Input Dataset step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files.

[galaxy-dev] can not login to workflows after postgresql setup

2012-07-04 Thread J.W.F.van_der_Heijden
Hi all, I have set up postgresql to work with galaxy because the standard mysqlite didn't work with my workflow. Now that postgresql seems to be working I can not login to galaxy. When I try to login it says that it can't find my username. And also when I click forgot password it says: Mail

Re: [galaxy-dev] Liftover tool installation woes

2012-07-04 Thread Jennifer Jackson
Hello Kwon, Most of this sounds correct. The only issue is with compressed files. Galaxy uses uncompressed liftOver data at our site and this is how we instruct that it be set up (see galaxy-central/tool-data/liftOver.loc.sample). Would you be able to run a test to see if uncompressing

Re: [galaxy-dev] can not login to workflows after postgresql setup

2012-07-04 Thread J.W.F.van_der_Heijden
Hi all, I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Also it seems that I am no longer able to upload files. It's only a 300kb test file

Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch

2012-07-04 Thread Dannon Baker
In your workflows, are you using Input Dataset steps? Galaxy uses these steps to know how to map datasets to do special things like this. If you're not currently using them, just open the workflow editor and add input dataset steps (it's at the very bottom of the tool list) connected to the

Re: [galaxy-dev] Question about compressed files

2012-07-04 Thread Jeremy Goecks
When using the 'upload via filesystem path' option for data libraries, Galaxy will use the file as is without decompressing it. In practice, this means that you'll need to decompress it before uploading it to a library because Galaxy tools expect the dataset to be uncompressed. This is, of

Re: [galaxy-dev] can not login to workflows after postgresql setup

2012-07-04 Thread Jeremy Goecks
I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in

Re: [galaxy-dev] Question about compressed files

2012-07-04 Thread Ciara Ledero
Thank you for explaining it further, Jeremy. We'll keep that in mind next time we use that method. Anyway, I'm sorry for this redundant post, but I'm getting an error every time I am uploading a file into a data library using my non-admin user account. Galaxy says that there is no valid file

Re: [galaxy-dev] Liftover tool installation woes

2012-07-04 Thread Kwon SoonJae
Hi Jen, Thanks for looking into this. I have unzipped all the .gz files so that the directory contains all .chain files. The liftover.loc file has also been modified to refer to all the .chain files instead, as such: http://pastebin.com/xSKGvUtG I still run into the same error if I try to run

[galaxy-dev] conflicting migration files

2012-07-04 Thread Langhorst, Brad
When I merged brad chapmans code into galaxy-central two 0099 migration files are created. I got things working by moving the ngs lims one to 0104 , but now i think i'll be in for a problem when a new 104 is created... What's the right way to solve this? Brad -- Brad Langhorst