Gerrit Botha's activity
From 03/20/2018 to 04/18/2018
04/17/2018
- 02:26 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Katie.
It seems like I found the issue why it was not submitting to PBS. The ```executer``` setting should have...
04/16/2018
- 05:05 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- For now I do not think we will make changes on the main code. So yes, all that we would need to do is merge the main ...
- 04:44 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Katie,
Everything is on the ```dev``` branch: https://github.com/uct-cbio/RNAseq/tree/dev . So should things no...
04/12/2018
- 05:04 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Katie,
I did the following.
1. Made a fork of the stable RNASeq pipeline to here: https://github.com/uct-cbi...
04/11/2018
- 02:26 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- Ok
- 02:22 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- Hi Katie,
I picked up this message from you on the bst-redmine@cbio.uct.ac.za account.
*"Gerrit this was wit... - 01:26 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- Jon this message is from Nicky.
"Ok so the evaluation is done already. We need to decide if we need to make use of... - 11:41 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Katie if this is the Docker file you are using https://github.com/ewels/nf-core-RNAseq/blob/master/Dockerfile you wou...
- 11:18 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- OK that is fine Katie.
Just on the overlay issue. Overlayfs is only available for kernel 3.18 or higher: https://w... - 10:55 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Katie,
1. Can you please point me to the Docker / Singularity file on GitHub which you have an issue with?
2...
04/10/2018
- 02:22 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- So what happens if you do use the ```--size``` flag with a rough estimate of the container size?
Ok, try running t...
04/09/2018
- 04:37 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- We had a BST meeting. Seems like there is a slight diversion from the original plan and suggestions made. Maybe bette...
- 11:43 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Try again. I opened up read permissions to the binary.
- 10:59 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Ok it is setup in ```/opt/exp_soft/cbio/nextflow```
Add the following lines in your ```.bashrc```
~~~
JAVA_C... - 10:09 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30 (In Progress): Update Nextflow to version 0.27.6
- Ok Katie, will do it in the next hour or so. Will get back to you.
- 11:08 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Katie,
Initially asked me if the info you are planning to share in this ticket should go in the ticket or on th...
03/28/2018
- 04:42 PM Setting up the BST helpdesk Feature #29: Create list of research groups to appear for ticket submission.
- The divisions/research groups we have worked with before not in the above the list should definitely be added. A brea...
03/26/2018
- 05:41 PM Setting up the BST helpdesk Feature #11: Add email system
- Email address should be bst-helpdesk@cbio.uct.ac.za
- 03:38 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- Hi Katie,
Can you please add any info you have on the setup you have at Hex?
Also for who did you plan to setup... - 03:36 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27 (New): What we already know and have setup
- Jairam Lingappa vissited Heather's group last year and was planning to setup an metagenome assembly pipeline on Hex. ...
03/22/2018
- 01:22 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- Ok
03/20/2018
- 12:02 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- Hi Jon,
Just want to check how it is going with this and if you need any help?
Regards,
Gerrit
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