Redmine

04/17/2018

04:51 PM Setting up the BST helpdesk Feature #33 (In Progress): Adding time tracking to the tickets

A potential option is to have a keyword in the ticket comment that can be picked up and parsed by a function. This me... Jon Ambler

04:45 PM Setting up the BST helpdesk Feature #33 (Resolved): Adding time tracking to the tickets

In order to be able to repost the time we responding on different tasks, we need to be able to log time spent on tick... Jon Ambler

04:42 PM Setting up the BST helpdesk Feature #29 (Closed): Create list of research groups to appear for ticket submission.

Jon Ambler

04:42 PM Setting up the BST helpdesk Feature #11 (Closed): Add email system

Jon Ambler

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... Gerrit Botha

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 ... Gerrit Botha

04:50 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

Aha, yes you're right - if we specify -r dev with the run (using our repo fork) it does pick up the uct_hex profile. ... Katie Lennard

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... Gerrit Botha

04:31 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

Gerrit I see even though you noticed that the uct_hex.conf was only on the dev branch it looks like the master branch... Katie Lennard

03:55 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

I've tested the custom build singularity image described above. This specific repository (https://github.com/nf-core/... Katie Lennard

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. Katie Lennard

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... Gerrit Botha

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 Gerrit Botha

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.
Katie Lennard

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... Gerrit Botha

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... Gerrit Botha

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 ... Jon Ambler

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... Gerrit Botha

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... Katie Lennard

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... Katie Lennard

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... Gerrit Botha

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... Katie Lennard

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... Gerrit Botha

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... Katie Lennard

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... Gerrit Botha

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... Katie Lennard

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... Gerrit Botha

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, ... Katie Lennard

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... Katie Lennard

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. Gerrit Botha

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:... Katie Lennard

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 ```... Katie Lennard

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... Gerrit Botha

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. Gerrit Botha

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) Katie Lennard

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. Jon Ambler

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... Katie Lennard

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... Gerrit Botha

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

Katie Lennard

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... Gerrit Botha

04:15 PM Setting up the BST helpdesk Feature #29 (In Progress): Create list of research groups to appear for ticket submission.

Jon Ambler

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... Jon Ambler

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... Jon Ambler

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 ... Jon Ambler

04:11 PM Setting up the BST helpdesk Feature #11 (In Progress): Add email system

Jon Ambler

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 Gerrit Botha

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... Gerrit Botha

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. ... Gerrit Botha

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 Gerrit Botha

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.
Jon Ambler

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 Gerrit Botha