# Bonus tips ### 🌈 Colored Logs with Batch Systems

Default: No colored logs

Colored unbuffered logs

When running jobs using batch systems like LSF or Slurm, many programs detect whether their output is being sent to a terminal (`TTY`) or a file and may disable features like color formatting or progress bars if they detect non-interactive output. One workaround, using it carefully, is to use the [`unbuffer`](https://manpages.debian.org/stretch/expect/unbuffer.1.en.html) utility from the `expect` package. `unbuffer` simulates a terminal by running the program in a pseudo-terminal (PTY), tricking the program into thinking it is running interactively in a terminal, so it continues to produce colored output. {% hint style="success" %} **Requirements:** * Have **`unbuffer`** available. See tips on [how to install on an HPC](#bonus-tip-install-unbuffer-in-an-hpc-with-miniconda). * **`unbuffer: True`,** in your `isabl_cli`s **`SUBMIT_CONFIGURATION`**. * **`>=0.3.28`** version of **`@papaemmelab/isabl_web`** * [8c8ad75](https://github.com/papaemmelab/isabl_cli/commit/8c8ad75c85b6c86f291787fcfbf4a51532930154) commit of **`isabl_cli`** {% endhint %} {% hint style="warning" %} Unbuffered output will redirect both stdout/stderr to the same`head_job.log`file, causing the file `head_job.err` output to be empty from errors of the running application. {% endhint %} {% hint style="danger" %} By simulating a pseudo-PTY, you can gain desired colored outputs, but some outputs like progress bars print undesired characters that can clutter your logs. Be aware to disable those if possible (i.e. `toil ... --disableProgress),`or for specific applications add a dummy env`TERM=dumb` to tell the program there's no effective terminal attached. {% endhint %} #### **âž• Bonus tip**: **Install `unbuffer` in an HPC with miniconda.** ```bash conda create -n myenv conda activate myenv conda install -c conda-forge expect ``` Having `$OPT_DIR` where you install your packages and `$BIN_DIR` where you add your executable binaries, create a runnable script called `unbuffer`, where you add your miniconda env's `unbuffer` executable and add its shared libraries: {% code title="${BIN\_DIR}/unbuffer" %} ```bash #!/bin/bash OPT_DIR= export LD_LIBRARY_PATH="${OPT_DIR}/miniconda3/envs/myenv/lib:$LD_LIBRARY_PATH" ${OPT_DIR}/miniconda3/envs/myenv/bin/unbuffer "$@" ``` {% endcode %} Test it works: ```bash $ unbuffer echo "Hello World!" Hello World ``` ### :dna: Use IGV links to be 1-click away to visualize your mutation calls \ The frontend allows the user to visualize alignment files (`bam`/ `cram`) through IGV, by using the API's `igv` endpoints in 2 cases: * `/api/v1/experiments/igv/{system_id}?assembly={assembly}&locus={locus}`: To visualize an aligned file stored in the`Experiment.bam_files` * `/api/v1/analyses/igv/{pk}?result={result}&result_index={result_index}&locus={locus}`: to visualize an analysis result whose `frontend_type` is `igv_. See` [`Frontend Result Types`](/writing-applications.md#frontend-result-types) But you can also use these endpoints widely to dynamically create your own **igv links**, when doing data analyses or creating reports! #### Demo time This is a cool example where you can generate clickable links in jupyter to visualize fusions events. The idea is to be 1-click away to visualize the reads of a specific sample in the locus of interest to see if a mutation is a real event or not. Taking into account that the param variable `locus` supports multiple locus for example to visualize the 2 breakpoints of the fusion. Each locus, creates a new igv view in a tab. The locus can be defined by adding multiple ones separated by a space.

Create IGV links in a Jupyter Notebook

Here you have an **IGV link** for each event. For example, clicking in the `GTF2I::GTF2IRD1`fusion link, will open an IGV where you can visualize the 2 breakpoints:\ \ `https://{my-instance}/api/v1/experiments/igv/{system_id}?assembly={assembly}&locus={locus1}%20{locus2}` {% hint style="info" %} `%20` is the safe url encoding for a `space` character, needed to append multiple locus. {% endhint %}

Visualize events pointing to the desired locus. Example showing aGTF2I::GTF2IRD1fusion in 2 locus at 7:74125440and 7:74015371

This feature is extremely powerful and useful, especially for generating reports with tens or thousands of variants. You can click on any variant to visualize it in IGV! --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.isabl.io/bonus-tips.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.