Running on singularity

[merytouceda]

Hi,

I am trying to run BiG-MEx in the HPC of my university, which instead of docker uses singularity. I was wondering if you could add to the wiki an example of running run_bgc_dom_annot.bash by calling docker from singularity.
Thanks!

[pereiramemo]

I am happy to read you are interested in our tool.
Yes, it will be convenient to have an option to run BiG-MEx with singularity; however, it will take some days until I can dedicate the time to properly have this.

In case it helps: I can send you the UProC database of BGC domains, so that you run the domain annotation on your server (basically, all that the bgc_dom_annot.bash does is to annotate the BGC domains with UProC).

UProC: http://uproc.gobics.de/

Cheers,

Emiliano

[merytouceda]

Thanks!

I think I will wait until it is possible to run BiG-MEx with singularity.

[shunido]

Hi @pereiramemo

I am interested too !
Did you got any luck on this ? to make it run under singlilarity?

Or can we have the minks to the containers so we pull them directly using singularity ?

Thanks

[pereiramemo]

Hi Shuindo,

I am glad to read you are interested in BiG-MEx.
I will make time next month to create the singularity images. This will be the easiest.
Hope this helps.
Cheers,

Emiliano

[pereiramemo]

Hi,

I created a new version of the scripts to run BiG-MEx using singularity. Also, I took the chance to make an important update: now the BGC domain annotation and counts profiling, and class abundance profiling, are integrated into a single tool: bgc_profiler.

Please note that I am still testing the tool. If you happen to find any issues please let me know.

I hope you find this useful.

Best,

Emiliano

[merytouceda]

Hi! Thanks so much for keeping me posted on this. I will be coming back to this soon and will inform you of any issues. Best, María Touceda Suárez Graduate Research Associate Barberán Lab Department of Environmental Science, University of Arizona ***@***.*** ***@***.***> Pronouns: She/Her/Hers barberanalbert.wixsite.com/labpage/people

…

On Feb 9, 2022, at 6:40 AM, Emiliano Pereira Flores ***@***.*** ***@***.***>> wrote: Hi, I created a new version of the scripts to run BiG-MEx using singularity. Also, I took the chance to make an important update: now the BGC domain annotation and counts profiling, and class abundance profiling, are integrated into a single tool: bgc_profiler. Please note that I am still testing the tool. If you happen to find any issues please let me know. I hope you find this useful. Best, Emiliano — Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHD2U3H7QFLNF3YCHVMIFILU2JVGBANCNFSM42IANAHQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.