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https://github.com/boutroslab/cld_docker

Docker for CRISPR Library Designer | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0915-2
https://github.com/boutroslab/cld_docker

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Docker for CRISPR Library Designer | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0915-2

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[![DOI](https://zenodo.org/badge/20669/fheigwer/cld.svg)](https://zenodo.org/badge/latestdoi/20669/fheigwer/cld)



# CRISPR Library Designer (CLD): a software for the multispecies design of sgRNA libraries



### Citation



[F. Heigwer\*, T. Zhan\*, M. Breinig, J. Winter, D. Brügemann, S. Leible, M. Boutros, CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries, Genome Biol., 2016, DOI:10.1186/s13059-016-0915-2](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0915-2 "Access manuscript directly")



### Abstract



Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs.



### Quick Start:



Also check out the pre-built docker at [dockerhub](https://hub.docker.com/r/boutroslab/cld_docker).



Install docker to the point that `docker run hello-world` runs successfully and use `cld` as described below e.g:



1. To use the graphical interface:



	1. Mac:



		1. Install xquartz: https://www.xquartz.org/

		2. `open -a XQuartz`

		3. `IP=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')`

		4. `xhost + $IP`

		5. adapt `docker-compose.yaml` change to folder and enter

			  

		```bash

		docker-compose up

		```



		or enter 



		```bash

		docker run -e DISPLAY=$IP:0 -v ${PWD}:/data boutroslab/cld_docker cld_gui

		```

			  

	2. Windows:

	

		1. Install a command line package manager for windows: https://chocolatey.org/

		2. Follow this guide to install the graphical interface manager for windows: https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde

		3. adapt `docker-compose.yaml` change to folder and enter 



		```bash

		docker-compose up

		```



		or enter 



		```bash		  

		docker run -e DISPLAY=:0.0 -v ${PWD}:/data boutroslab/cld_docker cld_gui

		```

			  

	3. GUIed linux:

	

		1. adapt `docker-compose.yaml` change to folder and enter 

			  

		```bash		  

		docker-compose up

		```



		or enter 



		```bash

		docker run -e DISPLAY=:0.0 -v ${PWD}:/data boutroslab/cld_docker cld_gui

		```

		2. When logging in remotely: log into your remote server by `ssh -X`



2. Download the database for your organism of interest.



```

docker run -v ${PWD}:/data boutroslab/cld_docker cld --task=make_database --output-dir=/data --organism homo_sapiens

```



3. Enter its name in the reference organism field on the start page.

4. Enter a list of gene identifiers in the "Gene List" tab and go to the "Design Parameter" tab to set your parameters.

5. Go to the "Start Analysis" tab to start sgRNA search.

6. The results will be created in the selected output directory ("Input/Output" tab).



**Command-Line-Start:**



Install docker to the point that docker run hello-world runs successfully and use cld as described below e.g:



```bash

docker run -v ${PWD}:/data boutroslab/cld_docker cld --help

```



cld can be called either with “--version”, printing its version number and copyrights, 

"--help" printing a more elusive help documentation and with “--task”. 



---

**NOTE**



The output directory defaults to `/data` within the Docker container. 

You can overwrite this by setting `--output-dir` to any other directory

within the container. Make sure that you mount your local directory to the

output directory when use run the Docker container: e.g. `-v ${PWD}:/data`



---



EXAMPLE to execute from the path containing all needed files:



```bash

docker run -v ${PWD}:/data boutroslab/cld_docker cld --task=end_to_end --output-dir=/data --parameter-file=/data/params.txt --gene-list=/data/gene_list.txt

```



cld can run 2 distinct tasks, database creation and 

library design.



Database creation is called using the `--task=make_database` command 

	giving the organism name of interest, as it is denoted in ENSEMBLs ftp folder structure

	e.g. homo_sapiens, and the rsync url to the current ftp server of ENSEMBL, examples 

 	can be found when cld  --help is called. After calling this function CLD will 

 	automatically download the latest toplevel FASTA, GFF and GTF files for the organism 

 	of interest and compile a database containing bowtie indexes, mygff files and 

 	reformatted sequence files. If not enough computing power is available to the user, 

 	these databases also might be downloaded from [here](http://www.e-crisp.org/E-CRISP/CLD-DB/). 



Library design can either be done in two steps: 



```bash

cld --task=target_ident

```



and then 



```bash

cld  --task=library_assembly

```

if the user wants 

to separate the two steps for example in order to only identify target sites without 

compiling a clonable library. 

Else 

	

```bash

cld  --task=end_to_end

```



which automatically will perform the steps mentioned before 

and present the end-result in a user defined output folder. 

For reasons of manageability for high throughput design, output files are kept 

as simple and standardised as possible. However a genome wide library targeting 

the human genome quickly spans several GB depending on how strict the parameters 

are chosen. Since the end_to_end task takes most time we benchmarked its time 

consumption to be approximately 1 h wall-time for an 8-core cpu node.



 	

For running cld from the command line the syntax as outlined in the [MANUAL](https://github.com/boutroslab/cld_docker/blob/master/MANUAL.md) must be used.