Redmine

04/20/2018

03:35 PM Setting up a portable metagenome assembly pipeline for CBIO Support #38 (New): How to download SRA files to hex

How to download input files (testdata) from SRA to hex:
Use sra-tools installed on hex (activate by doing ‘load modu... Katie Lennard

04/16/2018

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

04:31 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

04/11/2018

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

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

11:11 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

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

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

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

11:38 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

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

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

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