SEA-PHAGES | All posts created by akapinos

Link to this post \| posted 18 Feb, 2021 20:43
akapinos	Looks to me like that worked, thank you so much! For some reason, the program was no longer opening in the VM. In case it would be helpful to anyone else, I had to remove the program/master file and redownload the phamnexus-master.zip file from github. I was getting an error that the directory /seafaculty/home/phamnexus was 'not found' when trying to open the program, but it worked again after renaming the master file 'phamnexus' and moving it to the home folder. We downloaded the updates from Phamerator using the new database website (server 'HTTP://databases.hatfull.org/Actino_Draft/', using 'Actino_Draft' for the database) and now both Phamerator and PhamNexus are using Actino_Draft ver. 394 after checking for database updates in PhamNexus and entering the MySQL login info. Thank you again!

Link to this post | posted 18 Feb, 2021 20:43

Looks to me like that worked, thank you so much!

For some reason, the program was no longer opening in the VM. In case it would be helpful to anyone else, I had to remove the program/master file and redownload the phamnexus-master.zip file from github. I was getting an error that the directory /seafaculty/home/phamnexus was 'not found' when trying to open the program, but it worked again after renaming the master file 'phamnexus' and moving it to the home folder. We downloaded the updates from Phamerator using the new database website (server 'HTTP://databases.hatfull.org/Actino_Draft/', using 'Actino_Draft' for the database) and now both Phamerator and PhamNexus are using Actino_Draft ver. 394 after checking for database updates in PhamNexus and entering the MySQL login info.

Thank you again!

Posted in: Bioinformatic Tools and Analyses → PhamNexus on SEA-VM

Link to this post \| posted 17 Feb, 2021 01:18
akapinos	Hello! We are still using PhamNexus on the 2017 version of the SEA-VM to generate Nexus files for input to SplitsTree. Given the recent changes to the location of the Actino_Draft database, we're having some difficulties connecting the PhamNexus platform to new versions of the database (but were able to reconnect the SEA-VM version of Phamerator to the new database). Are there any quick fixes that would allow us to query the SQL Actino_Draft database on the SEA-VM version of PhamNexus/are there any alternative methods for generating nexus files containing pham data? Any help would be so appreciated! Thank you

Link to this post | posted 17 Feb, 2021 01:18

akapinos

Hello!

We are still using PhamNexus on the 2017 version of the SEA-VM to generate Nexus files for input to SplitsTree. Given the recent changes to the location of the Actino_Draft database, we're having some difficulties connecting the PhamNexus platform to new versions of the database (but were able to reconnect the SEA-VM version of Phamerator to the new database). Are there any quick fixes that would allow us to query the SQL Actino_Draft database on the SEA-VM version of PhamNexus/are there any alternative methods for generating nexus files containing pham data?

Any help would be so appreciated! Thank you smile

Posted in: Bioinformatic Tools and Analyses → PhamNexus on SEA-VM

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