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Update ucl_myriad.md #712

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26 changes: 26 additions & 0 deletions docs/ucl_myriad.md
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Expand Up @@ -22,6 +22,8 @@ export APPTAINER_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.apptainer/localcache
export APPTAINER_PULLFOLDER=/home/<YOUR_ID>/Scratch/.apptainer/pull
```

**Warning**: You may need to outcomment any singularity environmental variables you have set previously.

### Nextflow

Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (https://github.com/nextflow-io/nextflow/releases), you can then manually set this by entering (`NXF_VER=XX.XX.X`).
Expand All @@ -40,3 +42,27 @@ Then make sure that your bin PATH is executable, by placing the following line i
```bash
export PATH=$PATH:/home/<YOUR_ID>/bin
```

### Common troubleshooting issues:

1. If your job gets terminated by SIGHUP, you should then submit your nextflow script within a job:

`qsub -l h_rt=48:00:00 -l mem_free=40G -pe smp 1 -b y nextflow run`
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Suggested change
`qsub -l h_rt=48:00:00 -l mem_free=40G -pe smp 1 -b y nextflow run`
```bash
qsub -l h_rt=48:00:00 -l mem_free=40G -pe smp 1 -b y nextflow run
```

gives you a nice copy-code button


2. If a job fails due to apptainer requiring too much cpu/memory, from the `mksquashfs` process.

Then make a sge qsub script to pull the container using apptainer, then point to the location of the resultant SIF files.
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Then make a sge qsub script to pull the container using apptainer, then point to the location of the resultant SIF files.
Make a sge qsub script to pull the container using apptainer, then point to the location of the resultant SIF files.


e.g.

```bash
#!/bin/bash -l
#$ -l h_rt=3:0:0
#$ -l mem=50G
#$ -N Apptainer_pull
#$ -wd /home/<YOUR_ID>/Scratch/
#$ -e /home/<YOUR_ID>/Scratch/

# Pull a container.
apptainer pull docker://kanghu/hite:3.2.0
```
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