diff --git a/doc/getting_started.md b/doc/getting_started.md index 8a601a98566a4285e5eb574a6d9667a64b201a92..3b62c7a31195f5df236d5bb0eab9a0a3c363f499 100644 --- a/doc/getting_started.md +++ b/doc/getting_started.md @@ -79,7 +79,7 @@ If the containers are not found locally, they are automatically downloaded befor To have access to `charliecloud` on the PSMN you need to add the followin path to your `PATH` variable: -```` +```sh PATH=/Xnfs/abc/charliecloud_bin/:$PATH ``` @@ -87,7 +87,6 @@ You can add this line in your `~/.bashrc` or `~/.zshrc` file When running `nextflow` on the PSMN, we recommend to use `tmux` before launching the pipeline: - ```sh tmux ./nextflow src/solution_RNASeq.nf --fastq "data/tiny_dataset/fastq/tiny2_R{1,2}.fastq.gz" --fasta "data/tiny_dataset/fasta/tiny_v2_10.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -profile psmn @@ -104,4 +103,7 @@ You can edit the `src/ccin2p3.pbs` file to personalize your `nextflow` command a ```sh qsub src/ccin2p3.pbs ``` -```` + +``` + +```