Nowlan Freese added a comment - 05/Dec/19 3:48 PM DREME app has been updated by CyVerse. An IGB copy of the DREME app has been created and shared with the CyVerse team. Documentation for how to run the DREME motif finder have been added to the Terrain API Documentation. Closing issue.

Nowlan Freese added a comment - 05/Dec/19 3:46 PM Nowlan, I am sorry it has taken so long, but I think my colleague Amanda has managed to get the dreme app working. She will be testing it and making it public soon. Perhaps check the DE on Monday or Tuesday and try it out! Ramona – Ramona Ramona from CyVerse On Fri, Aug 9, 2019 at 09:21 AM, "Nowlan Freese" <nfreese@uncc.edu> wrote: Hi Ramona, I'm sorry to hear that Dreme software has been problematic. Thank you for continuing to look into it, it would be great to be able to use in CyVerse! We're still a couple weeks away from when we would need to use it, so no immediate rush! Best, Nowlan On Thu, Aug 8, 2019 at 11:57 PM, "Ramona Walls" <ramona.walls@cyverse-e884fe267ef0.intercom-mail.com> wrote: Nowlan, We have spent quite a bit of time trying to build a docker container for Dreme. Although we are able to build it locally and on Atmosphere, we get repeated (and inconsistent) errors when trying to build it with Docker. I will continue to investigate, and contact the Meme creators if need be, but I wanted to let you know the reason for the prolonged delay. Ramona On Tue, Jul 30, 2019 at 04:13 PM, "Nowlan Freese" <nfreese@uncc.edu> wrote: Thank you! On Tue, Jul 30, 2019 at 03:41 PM, "Ramona Walls" <ramona.walls@cyverse-e884fe267ef0.intercom-mail.com> wrote: Our student has been able to build a docker file, but he is still having problems getting it to build the way it should. I am helping him to troubleshoot now, and if we can't solve the problem in a day or two, I will pull in one of our developers and update you. Thank you for your patience. Ramona On Fri, Jul 26, 2019 at 09:11 AM, "Nowlan Freese" <nfreese@uncc.edu> wrote: Hi Ramona, Any updates on the new DREME app? Thanks! Nowlan On Wed, Jul 10, 2019 at 03:40 PM, "Nowlan Freese" <nfreese@uncc.edu> wrote: No problem, I was also on holiday! Thank you so much for working on this for me! On Tue, Jul 9, 2019 at 05:44 PM, "Ramona Walls" <ramona.walls@cyverse-e884fe267ef0.intercom-mail.com> wrote: Hi Nowlan. Sorry for the delay. I am back fro vacation now, and I have a student working on the new DREME app. On Tue, Jul 2, 2019 at 09:19 AM, "Nowlan Freese" <nfreese@uncc.edu> wrote: Hi Ramona, The current public version of the DREME app works perfectly fine for me except for one problem: the inputs section requires a negative sequence. I think this was a mistake, as the tooltip states: "Negative control sequences. The positive sequences are shuffled to create the negative set if this is not specified." This indicates to me that the Negative sequence input should not have been set as required. And because the tool itself is considered deprecated, I cannot make my version of the app public. Nowlan On Mon, Jul 1, 2019 at 10:15 PM, "Ramona Walls" <ramona.walls@cyverse-e884fe267ef0.intercom-mail.com> wrote: Nowlan, I will work on updating this tool as soon as I am back from vacation next week. Ramona Are there specific parts of this tool that you want to use? Ramona On Wed, Jun 19, 2019 at 10:49 AM, "Operator" <operator@cyverse-e884fe267ef0.intercom-mail.com> wrote: CyVerse will be back in 2 hours. You'll be notified here and by email (nfreese@uncc.edu) On Wed, Jun 19, 2019 at 10:49 AM, "Nowlan Freese" <nfreese@uncc.edu> wrote: Hi, I'm using the DREME app by Matthew Vaughn, and I need to make a copy in order to make some edits, but would then like to make that public. However, I'm getting the message "This app uses a deprecated tool. You can still edit and use this private app, but you will have to choose a newer version of the tool before it can be made public." It looks like the MEME suite is now on version 5.0.5 ( http://meme-suite.org/doc/download.html ). Could someone update this tool so that I can make the app public? Thanks!