Activity
From 03/15/2018 to 04/13/2018
04/12/2018
- 05:28 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Thanks Gerrit, much appreciated - I'll go through this and do some testing on the new image.
- 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
- 02:25 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- No problem Gerrit. No, Jai only got as far as asking Andrew to install the necessary software.
- 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... - 12:56 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
- I found out that they have already compared Dragen to GATK and BWA using the Platinum genomes trio, the accuracy and ...
- 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...
- 11:28 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Katie Lennard wrote:
> Oh dear..Ok we'll have to get rebuild the image then I guess..See latest response from Phil o... - 11:23 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Oh dear..Ok we'll have to get rebuild the image then I guess..See latest response from Phil on this https://github.co...
- 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... - 11:11 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Gerrit,
At the moment the main problem is that I can't download the development version of the Singularity imag... - 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
- 05:33 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Gerrit Botha wrote:
> So what happens if you do use the ```--size``` flag with a rough estimate of the container siz... - 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... - 01:41 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Development branch with custom 'uct_hex' profile up and running but having issues with the singularity image specifie...
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...
- 12:56 PM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Katie Lennard wrote:
> Gerrit Botha wrote:
> > Try again. I opened up read permissions to the binary.
>
> Hmmm, ... - 12:54 PM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Gerrit Botha wrote:
> Try again. I opened up read permissions to the binary.
Hmmm, kry nou:
Downloading nextflow... - 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.
- 11:38 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Have added lines to .bashrc but can't test nextflow (version -v):
/bin/bash: /opt/exp_soft/cbio/nextflow/nextflow:... - 11:13 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Gerrit Botha wrote:
> Ok it is setup in ```/opt/exp_soft/cbio/nextflow```
>
> Add the following lines in your ```... - 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.
- 09:51 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30 (In Progress): Update Nextflow to version 0.27.6
- The RNAseq pipeline requires an updated version of Nextflow (currently 0.26.3, need 0.27.6)
- 12:32 PM Setting up the BST helpdesk Feature #29 (Resolved): Create list of research groups to appear for ticket submission.
- The research group menu has been updated with the group found in the link above.
- 11:14 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Gerrit Botha wrote:
> Hi Katie,
>
> Initially asked me if the info you are planning to share in this ticket shoul... - 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...
04/06/2018
- 03:38 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25 (In Progress): Configure NGI-RNAseq pipeline to run on hex
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...
- 04:15 PM Setting up the BST helpdesk Feature #29 (In Progress): Create list of research groups to appear for ticket submission.
- 04:15 PM Setting up the BST helpdesk Feature #29 (Closed): Create list of research groups to appear for ticket submission.
- A list of research groups to be included in the ticketing system needs to be agreed upon.
This will serve to keep... - 04:18 PM Setting up the BST helpdesk Feature #12 (In Progress): Add more info in knowledge base categories
- At the meeting, the person responsible for each category was assigned. Team members are currently adding the informat...
- 04:12 PM Setting up the BST helpdesk Feature #11 (Resolved): Add email system
- Email system is working, emails to the UCT outlook server was being blocked because the server address and email was ...
- 04:11 PM Setting up the BST helpdesk Feature #11 (In Progress): Add email system
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
- 11:02 AM 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 Gerrit,
I'm just waiting on the CPGR to give me a time to come in so they can show me the system.
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
03/15/2018
- 04:39 PM Setting up a portable RNA-Seq pipeline for CBIO Support #24: Setting up the NGI-RNAseq pipeline on UCT Hex
- Katie I've talked to Chris Fields he is working with Jenny. He will check if he can make their pipeline available. He...
- 03:07 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Katie just a note. The section `singularity.cacheDir = "/scratch/DB/bio/singularity-containers` in our `config.txt` i...
- 02:55 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25 (In Progress): Configure NGI-RNAseq pipeline to run on hex
- Pertinent points for setup of NGI-RNAseq pipeline on UCT hex
*Main pipeline source code is at https://github.com/Sci...
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