diff --git a/lectures/conda/conda.pdf b/lectures/conda/conda.pdf index 77720873..2559292c 100644 Binary files a/lectures/conda/conda.pdf and b/lectures/conda/conda.pdf differ diff --git a/lectures/containers/containers.Rmd b/lectures/containers/containers.Rmd index 3ddf99b1..574f19f0 100644 --- a/lectures/containers/containers.Rmd +++ b/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? + + + +In 2021 Singularity joined the Linux Foundation and became Apptainer. + +The company Sylabs still maintains **Singularity** + --- # Docker vs. Singularity diff --git a/lectures/containers/containers.pdf b/lectures/containers/containers.pdf index 51c411f6..8a10bdc1 100644 Binary files a/lectures/containers/containers.pdf and b/lectures/containers/containers.pdf differ diff --git a/lectures/rmarkdown/rmarkdown.pdf b/lectures/rmarkdown/rmarkdown.pdf index 10d92bca..676fe199 100644 Binary files a/lectures/rmarkdown/rmarkdown.pdf and b/lectures/rmarkdown/rmarkdown.pdf differ diff --git a/lectures/snakemake/snakemake.Rmd b/lectures/snakemake/snakemake.Rmd index 24aa3780..c37d2749 100644 --- a/lectures/snakemake/snakemake.Rmd +++ b/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[ - -`$ 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 diff --git a/lectures/snakemake/snakemake.pdf b/lectures/snakemake/snakemake.pdf index db029598..7018d339 100644 Binary files a/lectures/snakemake/snakemake.pdf and b/lectures/snakemake/snakemake.pdf differ diff --git a/pages/containers/containers-7-singularity.md b/pages/containers/containers-7-singularity.md index 7d0acd3f..dd2b2f71 100644 --- a/pages/containers/containers-7-singularity.md +++ b/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!**
+> 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 diff --git a/pages/course-information/pre-course-setup.md b/pages/course-information/pre-course-setup.md index e5d16aac..7f5133c1 100644 --- a/pages/course-information/pre-course-setup.md +++ b/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**
+> 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.