Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

2013-12-16 Thread Jennifer Jackson
Hello Javier, If you would like to see an enhancement for a tool that is sourced from the tool shed, then the repository author is the correct person to contact. Go to http://usegalaxy.org/toolshed and log in to see contact information. The repo name is bedtools. The Tool Shed also has an

[galaxy-dev] sort list of ftp uploaded files

2013-12-16 Thread Ulf Schaefer
Dear all Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the param type=ftpfile / tag unfortunately. If the user just selects all files they end

[galaxy-dev] cloudlaunch - Can't ssh or ping

2013-12-16 Thread greg
Hi guys, I just did a cloud launch of MSG by going here: https://usegalaxy.org/cloudlaunch I downloaded the pem file as instructed and I can access the galaxy admin page now. However when I try to ssh into it: $ ssh -i Downloads/cloudman_keypair.pem

Re: [galaxy-dev] cloudlaunch - Can't ssh or ping

2013-12-16 Thread greg
I last used cloud launch a year ago with this account. I may have used biocloudcentral though at that point. Is there a work around I can do in the meantime, or should I wait for your fix? On Mon, Dec 16, 2013 at 10:34 AM, Dannon Baker dannon.ba...@gmail.com wrote: Have you previously used

Re: [galaxy-dev] cloudlaunch - Can't ssh or ping

2013-12-16 Thread Dannon Baker
If this is an older account then it shouldn't be the VPC issue. I just attempted to ssh to it and it does respond fine for me -- what are the permissions for the cloudman_keypair.pem? `chmod 700 ~/Downloads/cloudman_keypair.pem` and try again. If that doesn't work, you may want to try using

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

2013-12-16 Thread Carlos Borroto
Hi Tim, This sounds great. I'll be happy to help testing and hopefully find some time to help packaging once it gets into Debian Med(are you submitting all your packages there?). One question, for apache/nginx configuration why not use something ala phpMyAdmin which ask you if you want to

Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

2013-12-16 Thread Jennifer Jackson
Javier, This is part of a tool repository that can be installed into a local, cloud, or slipstream Galaxy and used there. http://getgalaxy.org http://usegalaxy.org/cloud https://wiki.galaxyproject.org/BigPicture/Choices http://usegalaxy.org/toolshed

Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

2013-12-16 Thread Javier Simon-Sanchez
Hi Jennifer, Intersect_bed is exactly what I need. How can I include this on my workflows? (sorry for asking so many things. Im new with galaxy) From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Monday, December 16, 2013 4:03 PM To: Javier Simon-Sanchez; galaxy-...@bx.psu.edu Subject: Re: