Merge pull request #201 from NBISweden/devel

Devel

lectures/containers/containers.Rmd

@@ -259,6 +259,15 @@ an open source container platform suitable for HPC clusters
 
 >Singularity was created to run complex applications on HPC clusters in a simple, portable, and reproducible way.
 
+---
+# What is Apptainer?
+
+<img src="http://apptainer.org/static/hero-img-e614806cf573fd0cbbe09a25d9e69637.png" style="width:100%;"/>
+
+In 2021 Singularity joined the Linux Foundation and became Apptainer.
+
+The company Sylabs still maintains **Singularity**
+
 ---
 
 # Docker vs. Singularity

lectures/snakemake/snakemake.Rmd

@@ -120,7 +120,6 @@ done
 
 Using snakemake rules:
 
-
 ```python
 rule trim_fastq:
     output: temp("{prefix}.trimmed.fastq")
@@ -140,19 +139,19 @@ rule gzip:
 # Example: sequence trimming
 
 Using snakemake rules:
-
+.small[
 ``` bash
-$ snakemake {a,b}.trimmed.fastq.gz
+$ snakemake -c 1 {a,b}.trimmed.fastq.gz
 ```
-
+]
 ---
 
 # Example: sequence trimming
 
 Using snakemake rules:
-
+.small[
 ``` bash
-$ snakemake {a,b}.trimmed.fastq.gz
+$ snakemake -c 1 {a,b}.trimmed.fastq.gz
 Provided cores: 1
 Rules claiming more threads will be scaled down.
 Job counts:
@@ -174,19 +173,17 @@ rule gzip:
 Removing temporary output file a.trimmed.fastq.
 2 of 4 steps (50%) done
 ```
-
+]
 ---
 
 # Example: sequence trimming
 
 Using snakemake rules:
-
+.small[
 ``` bash
-$ snakemake {a,b}.trimmed.fastq.gz
+$ snakemake -c 1 {a,b}.trimmed.fastq.gz
 ```
-
 ...
-
 ``` bash
 rule trim_fastq:
     input: b.fastq
@@ -201,7 +198,7 @@ rule gzip:
 Removing temporary output file b.trimmed.fastq.
 4 of 4 steps (100%) done
 ```
-
+]
 ---
 
 # Piecing the rules together
@@ -231,28 +228,29 @@ than downstream files, so it reruns the necessary rules.
 
 .pull-right[
 <img src="dag1.png", width=100%>
-
-`$ touch intermediate/NCTC8325.1.bt2`
-
-`$ snakemake supplementary.pdf`
-
+.small[
+```bash
+$ touch intermediate/NCTC8325.1.bt2
+$ snakemake supplementary.pdf
+```
+]
 ]
 
 ---
 
 # Anatomy of a Snakemake rule
-
+.small[
 ``` python
 rule trim_fastq:
     output: temp("{prefix}.trimmed.fastq")
     input: "{prefix}.fastq"
     log: "logs/{prefix}.trim_fastq.log"
 ```
-
+]
 ---
 
 # Anatomy of a Snakemake rule
-
+.small[
 ``` python
 rule trim_fastq:
     output: temp("{prefix}.trimmed.fastq")
@@ -265,11 +263,11 @@ rule trim_fastq:
                     2> {log}
         """
 ```
-
+]
 ---
 
 # Anatomy of a Snakemake rule
-
+.small[
 ``` python
 rule trim_fastq:
     output: temp("{prefix}.trimmed.fastq")
@@ -288,11 +286,11 @@ rule trim_fastq:
                    2> {log}
       """
 ```
-
+]
 ---
 
 # Anatomy of a Snakemake rule
-
+.small[
 ``` python
 rule trim_fastq:
     output: temp("{prefix}.trimmed.fastq")
@@ -315,11 +313,12 @@ rule trim_fastq:
                    2> {log}
       """
 ```
-
+]
 ---
 
 # Anatomy of a Snakemake rule
 
+.small[
 ``` python
 rule trim_fastq:
     output: temp("{prefix}.trimmed.fastq")
@@ -346,7 +345,7 @@ rule trim_fastq:
                    2> {log}
       """
 ```
-
+]
 ---
 
 # Snakemake commandline

pages/containers/containers-7-singularity.md

@@ -37,6 +37,13 @@ images to the Singularity Image Format (SIF). This is great if there's a Docker
 image that you want to use on an HPC cluster such as Uppmax where you cannot use
 Docker.
 
+> **Tip!** <br>
+> If you are running singularity through Vagrant VirtualBox you may have to
+> set the temporary directory that Singularity uses during pull/build commands
+> to something with more disk space. First run `mkdir ~/tmp` to create a tmp 
+> directory inside the home folder of the VirtualBox, then 
+> `export SINGULARITY_TMPDIR="~/tmp"`.
+
 Let's try to convert the Docker image for this course directly from DockerHub
 using `singularity pull`:
 
@@ -67,7 +74,7 @@ Since Singularity bind mounts the current working directory we can simply
 execute the workflow and generate the output files using:
 
 ```bash
-singularity run --vm-ram 2048 mrsa_proj.sif
+singularity run mrsa_proj.sif
 ```
 
 This executes the default run command, which is

pages/course-information/pre-course-setup.md

@@ -54,8 +54,14 @@ resources:
 - [Installing and using Linux Bash on Windows](https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/)
 - [Installing Linux Bash on Windows](https://itsfoss.com/install-bash-on-windows/)
 
+> **Note** <br>
+> If you run into error messages when trying to download files through the Linux
+> shell (_e.g._ `curl:(6) Could not resolve host`) then try adding the Google
+> nameserver to the internet configuration by running `sudo nano /etc/resolv.conf`
+> then add `nameserver 8.8.8.8` to the bottom of the file and save it.
+
 Open a bash shell Linux terminal and clone the GitHub repository containing all
-files you will need for completing the tutorials as follows. First, `cd` into
+files you will need for completing the tutorials as follows. First, `cd` into
 a directory on your computer (or create one) where it makes sense to download
 the course directory.