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telatin committed Jun 7, 2024
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8 changes: 7 additions & 1 deletion _posts/2022-06-03-hpc.md
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Expand Up @@ -53,7 +53,13 @@ Both packages are experimental, one carries dbs the other will allow you to use

Following the [Vibrioi jascida pangenome](https://merenlab.org/tutorials/vibrio-jasicida-pangenome/), we downloaded the FASTA files and we want to filter them by length.

We can loop and use [`runjob`](https://metacpan.org/dist/NBI-Slurm/view/bin/runjob) to submit the job to the cluster:
We can loop and use [`runjob`](https://metacpan.org/dist/NBI-Slurm/view/bin/runjob) to submit the job to the cluster.

Basically you can run any command specifying the required resource like:

```bash
runjob -c 8 -m 12G "spades.py -s reads.fq..."
```

```bash
# You should be in an interactive session!
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31 changes: 21 additions & 10 deletions pages/about.md
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Expand Up @@ -10,16 +10,27 @@ This website collects and share information about the training and workshop acti

## Calendar

| Date | Workshop | Info |
|-----------------|------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------|
| 5 March | [Machine Learning]({{ site.baseurl }}{% post_url 2023-01-01-machine-learning %}): Seminar | [Intranet](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?mid=0) |
| 7 March | [Machine Learning]({{ site.baseurl }}{% post_url 2023-01-01-machine-learning %}): Workshop | [Intranet](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?mid=0) |
| 18-20 March | [nf-core hackathon]({{ site.baseurl }}{% post_url 2023-01-02-nf-core %}) | [nf-co.re](https://nf-co.re/events/2024/hackathon-march-2024/uk-norwich) |
| 26 March | [Statistical Analysis of the Microbiome]({{ site.baseurl }}{% post_url 2023-01-04-data-science %}) | [Intranet](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66081) |
| 8 May | [Protein bioinformatics and AI]({{ site.baseurl }}{% post_url 2023-01-20-proteins %}) | UG55B, 14.00 |
| 20-24 May | [Large Scale Analysis of Microbial genomes]({{ site.baseurl }}{% post_url 2023-01-10-large-scale %}) | In the page |
| June (1st week) | [Anvi'o Workshop]({{ site.baseurl }}{% post_url 2023-06-01-anvio %}) | In the page |
| June 25 | [MetaPhlAn and HuMANN]({{ site.baseurl }}{% post_url 2023-05-01-biobakery %}) | In the page |
| Date | Workshop | Info |
| -------------- | --------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------- |
| 5 March | [Machine Learning]({{ site.baseurl }}{% post_url 2023-01-01-machine-learning %}): Seminar | [Intranet](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66033) |
| 6 March | [Machine Learning]({{ site.baseurl }}{% post_url 2023-01-01-machine-learning %}): Networking sessions | |
| 7 March | [Machine Learning]({{ site.baseurl }}{% post_url 2023-01-01-machine-learning %}): Workshop | [Intranet](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66033) |
| 18 March | [nf-core hackathon]({{ site.baseurl }}{% post_url 2023-01-02-nf-core %}): introduction and docs | [nf-co.re](https://nf-co.re/events/2024/hackathon-march-2024/uk-norwich) |
| 19 March | [nf-core hackathon]({{ site.baseurl }}{% post_url 2023-01-02-nf-core %}): modules and hacking | [nf-co.re](https://nf-co.re/events/2024/hackathon-march-2024/uk-norwich) |
| 20 March | [nf-core hackathon]({{ site.baseurl }}{% post_url 2023-01-02-nf-core %}): future plans | [nf-co.re](https://nf-co.re/events/2024/hackathon-march-2024/uk-norwich) |
| 25 March | [Background on rarefaction](https://mcalgaro93.github.io/randomtopics/rarefaction-practice-in-microbiome-data-analysis.html) | [Notes](https://mcalgaro93.github.io/randomtopics/rarefaction-practice-in-microbiome-data-analysis.html) |
| 26-28 March | [Statistical Analysis of the Microbiome]({{ site.baseurl }}{% post_url 2023-01-04-data-science %}) with Dr. Calgaro | [Intranet](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66081) |
| 8 May | [Protein bioinformatics and AI]({{ site.baseurl }}{% post_url 2023-01-20-proteins %}) | UG55B, 14.00 |
| **20-24 May** | [**Large Scale Analysis of Microbial genomes**]({{ site.baseurl }}{% post_url 2023-01-10-large-scale %}) | In the page |
| 21st May, | [Workshop: Comparative Genomics of the Tree of Life](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66310) | UG55 ABC 9:30-12:00 |
| 21st May | [QIB Data Science group meeting](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66313) | UG55 AB , 14:00-16:30 |
| 22nd May | [Workshop: Petascale Structure Prediction and Phylogenetics](https://intranet.nbi.ac.uk/infoserv/cgi-bin/calendar/default.asp?id=66311) | UG55 ABC , 14:00-17:00 |
| **May-June** | [**Anvi'o Workshop**]({{ site.baseurl }}{% post_url 2023-06-01-anvio %}) | In the page |
| May 30 | Anvi'o: [Installation clinic]({{ site.baseurl }}{% post_url 2022-06-02-install %}) | UG55B-C 15:00-17:00 |
| June 4 | Anvi'o: Introduction and [Pangenome Analysis](https://merenlab.org/tutorials/vibrio-jasicida-pangenome/) | UG55B-C 13:30-17:00 |
| June 5 | Anvi'o: [from short reads to MAGs](https://anvio.org/learn/metagenomics/) | UG55B-C 13:30-17:30 |
| June 6 | Anvi'o: [Metabolism reconstruction](https://anvio.org/tutorials/fmt-mag-metabolism/) | UG55B-C 13:30-17:30 |
| June 25 | [MetaPhlAn and HuMANN]({{ site.baseurl }}{% post_url 2023-05-01-biobakery %}) | In the page |

## Topics

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