CIPRes+Analyses

=CIPRes Analyses=

[|CIPRes] (CyberInfrastructure for Phylogenetic Research) provides access to phylogenetic inference programs running on a fast computer. Zephyr provides a means to request that CIPRes conducts RAxML and GARLI runs remotely.

In order to use CIPRes, you will need an account on their REST server. You can register for an account here: https://www.phylo.org/restusers/register.action

To infer phylogenetic trees on CIPRes, choose Analyses>Tree Inference>Likelihood Tree Inference>**GARLI Likelihood [CIPRes]** or **RAxML [CIPRes]**. (You can also use CIPRes in the context of a SOWH test.) More details about about these analyses are provided on the GARLI and RAxML pages.

Reconnecting to CIPRes analyses
If you begin a GARLI or RAxML search on CIPRes, the Mesquite's log window will give information about the status of the analysis. If you save your file in Mesquite while the run is happening, and then quit Mesquite, when you next open the file in Mesquite Zephyr will attempt to reconnect with CIPRes again, and read in any available results.

Signing in to CIPRes
Before Mesquite can communicate to CIPRes, you will need to enter your CIPRes REST services username and password. Mesquite will query you whenever it needs the information, which will be once in each run of Mesquite (unless you specifically request to sign in again). The next time you start up Mesquite you will need to re-enter your information.

The dialog box you will be presented with looks like this:

If you don't have an account on CIPRes, you can touch the button and the CIPRes REST registration page will open in your web browser.

CIPRes Utilities
There are several tools available to allow you to manage your CIPRes analyses. With Mesquite's log window frontmost, there are the following entries under the CIPRes Utility menu of the Utilities menu:
 * **List Jobs**: will list all of your jobs run on CIPRes
 * **Job Status**: This will present a dialog box in which you can past the job's URL (e.g., https: //cipresrest.sdsc.edu/cipresrest/v1/job/DavidMaddison/NGBW-JOB-RAXMLHPC8_REST_XSEDE-FA04B71C24AF4D1F88456AA4C5CA3E78), and ask CIPRes the status of that job.
 * **Delete Job**: By pasting a job's URL into this dialog box, you can delete the job.
 * **Delete All Jobs**: will delete all of your jobs on CIPRes, including actively running jobs
 * **Download Files from Jobs**: By pasting a job's URL into this dialog box, you can ask CIPRes for all files associated with that job.