[galaxy-user] Secure file upload gateway for Galaxy

Hi, Our team at the University of Oslo is building a Life Science Portal based on Galaxy. We operate several standalone instances and we have the necessary sysadmin experience, but we really need to implement a more secure file upload mechanism than FTP (we do not like to send cleartext password c

[galaxy-user] Stitch MAF blocks

Hi, I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I h

Re: [galaxy-user] Secure file upload gateway for Galaxy

On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras wrote: > Hi, > > Do you have best recipes for SFTP/Aspera upload gateway integration to > Galaxy? We would welcome advise on that matter. > Hi, I haven't implemented yet, but I'm planning on using plain scp(windows user can use WinSCP). I shoul

Re: [galaxy-user] Metagenomic filtering

Jing et al Thank you for the offer to write some code to help advance the metagenomics arena. It is certainly needed. So the problem is well known with megablast and shotgun metagenomics and without proper understanding and correct software will yield very misleading and in many cases incorr

[galaxy-user] Need your helps about Galaxy

Dear Dannon, I built a new cloud Galaxy instance today. Would you please tell me how to transfer given accounts from an old Galaxy to this new one? This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ This is new Galaxy: http://galaxyclass.genenetwork.org/ Thanks a lot. Lei Yan Center fo

Re: [galaxy-user] Stitch MAF blocks

Hello, Yes, this tool functions on MAF input. For examples through several cases with this tool group, including this tool, please see: " Making whole genome alignments usable for biologists" publication & supplemental. https://main.g2.bx.psu.edu/u/dan/p/maf "Using Galaxy" publication & sup

Re: [galaxy-user] Need your helps about Galaxy

As I said before, there is no easy way to do this. You just need to dump the old database and load into the new database. I would suggest making a copy of the old database with a current version of Galaxy. The migration scripts will then bring it up to date so you will have identical schemas. You s

Re: [galaxy-user] Secure file upload gateway for Galaxy

Galaxy's FTP support uses ProFTPD, which has modules for both TLS (FTPS) and SFTP. -- James Taylor, Associate Professor, Biology/CS, Emory University On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras wrote: > Hi, > > Our team at the University of Oslo is building a Life Science Portal > based

Re: [galaxy-user] your video of using cloudman

Elwood: With large fastq files your best option will be either using public server (which is having difficulties today) or running a local instance of Galaxy. We are very much aware that the public site is not behaving well. It will be back on-line today and in the coming weeks we will be switchin

Re: [galaxy-user] Need your helps about Galaxy

Thanks, James. I worked it out by downloading my data files and workflow. For some reason MACS still doesn't work. Any ideas? Lawrence T Reiter, PhD UTHSC, Memphis, TN On Sep 24, 2013, at 11:32 AM, "James Taylor" wrote: > As I said before, there is no easy way to do this. You just need to > du

Re: [galaxy-user] Metagenomic filtering

Hi all - Not to derail the conversation, but I wanted to point out some Galaxy resources that may help when considering how to approach solution. These may be knowns, but thought I'd put them out there just in case. See below. Best! Jen Galaxy team There are at least three public Galaxy instan

Re: [galaxy-user] Need your helps about Galaxy

Hi Lawrence, What version of MACS are you running? The Galaxy wrapper in galaxy-dist supports v1.3. I am 99% certain that the latest Cloudman image is the same, but Dannon can correct me. The two Tool Shed repos for MACS support v1.4 and v2.0.10. Making sure that the wrapper & binary are a ma

Re: [galaxy-user] History will not load?

Hi Maria, Yes, this is a known issue and we have been working on resolving it today. A red banner is up on the public Main server with a description. That said, from my own testing when you first sent this in to a test I just did now, there appears to be some improvement already. When fully c

Re: [galaxy-user] de novo RNA-Seq workflow

Hi Carlos, We don't have a Trinity workflow available and I've looked through all of the donated community tutorials and have not been able to find one there, either. The Tool Shed has a newer feature that permits Workflow sharing, but that also lacks a RNA-seq assembly->analysis workflow. T