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@jwinter6
jwinter6 authored Nov 1, 2017
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Expand Up @@ -5,13 +5,6 @@ Welcome to the CRISPRAnalyzeR Github page!
CRISPRAnalyeR is a web-based, interactive suite for the analysis and documentation of pooled CRISPR Screens.


---

---
# Attention !

# CRISPRAnalyzeR Web-interface / Live Demo is OFFLINE for maintenance from 2017-10-04 until 2017-10-09

---

---
Expand Down Expand Up @@ -154,7 +147,15 @@ __It is your responsibility to obtain all required licenses in case of commercia


```
Version 1.20 (latest)
Version 1.40 (latest)
- added new library interface for pre-selection of screens
- added pre-made library re-evaluation for addgene-provide libraries
- fixed smaller bugs
- speed increase for some functions
- improved essential genes information
- added Advanced Options to skip FASTQ Quality Report, create own regular expression, use bad-quality libraries
Version 1.20
- added new user interface for data upload
- fixed many sgRNA libraries
- added Addgene sgRNA libraries for easier use
Expand Down Expand Up @@ -274,15 +275,15 @@ Open Kitematic and click on the CRISPRAnalyzeR image - you will see a SETTING bu
4. Open a terminal or command line (macOS: Terminal; Windows: cmd.exe)
4. Download and run the CRISPRAnalyzeR directly from the online repository (without additional settings)
```
docker run --rm -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -p 80:8000 boutroslab/crispranalyzer:latest
```
It is important to keep the __80:3838__ as this tells the software how to access it via the browser.
It is important to keep the __80:8000__ as this tells the software how to access it via the browser.
By default, CRISPRAnalyzeR can be accessed by the web-browser using __http://localhost/CRISPRAnalyzeR__.

If you want to run a specific version, just replace the `latest` with the specific version number

```
docker run --rm -p 80:3838 boutroslab/crispranalyzer:1.08
docker run --rm -p 80:8000 boutroslab/crispranalyzer:1.40
```

All pre-configured versions are listed at the [Docker Hub](https://hub.docker.com/r/boutroslab/crispranalyzer/tags/).
Expand Down Expand Up @@ -316,7 +317,7 @@ In case you would like to update CRISPRAnalyzer to the latest version, just type
to download the latest version and then run it as described above:

```
docker run --rm -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -p 80:8000 boutroslab/crispranalyzer:latest
```

## How to Start and Restart the CRISPRAnalyzeR
Expand Down Expand Up @@ -357,7 +358,7 @@ Be sure to hit the save button and start/restart CRISPRAnalyzeR.
All parameters can be set during the start by the following:

```bash
docker run --rm -e PARAMETER1 -e PARAMETER2 -e PARAMETER3 -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -e PARAMETER1 -e PARAMETER2 -e PARAMETER3 -p 80:8000 boutroslab/crispranalyzer:latest
```

this means you always need to add `-e` in front of the parameters, e.g.:
Expand All @@ -369,7 +370,7 @@ this means you always need to add `-e` in front of the parameters, e.g.:
e.g.

```bash
docker run --rm -e bowtie_threads=4 -e proxy_url="http://thisismyproxy.com" -e proxy_port=80 -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -e bowtie_threads=4 -e proxy_url="http://thisismyproxy.com" -e proxy_port=80 -p 80:8000 boutroslab/crispranalyzer:latest
```


Expand Down Expand Up @@ -439,7 +440,7 @@ docker build -t CRISPRAnalyzeR .
## Test the image

```bash
docker run --rm -p 80:3838 CRISPRAnalyzeR
docker run --rm -p 80:8000 CRISPRAnalyzeR
```

Check it by opening a browser tab and navigating to
Expand Down Expand Up @@ -473,7 +474,7 @@ In case you want to use the COSMIC database, please proceed as follows.
Please replace _*DATABASEFOLDER*_ byt the full path to the directory where you have placed the CosmicMutantExport.tsv!

```bash
docker run --rm -v *DATABASEFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/database -e COSMIC_database="CosmicMutantExport.tsv" -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -v *DATABASEFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/database -e COSMIC_database="CosmicMutantExport.tsv" -p 80:8000 boutroslab/crispranalyzer:latest
```

*Please note that the COSMIC database is loaded during the analysis procedure and requires 1 GB of RAM.*
Expand All @@ -483,7 +484,7 @@ Please replace _*DATABASEFOLDER*_ byt the full path to the directory where you
By default, CRISPRAnalyzeR has the Enrichr API access ENABLED.
You can DISBALE the Enrichr API access during the start by setting the paratemer __-e disable_EnrichR=TRUE__
```bash
docker run --rm -e disable_EnrichR=TRUE -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -e disable_EnrichR=TRUE -p 80:8000 boutroslab/crispranalyzer:latest
```

Please not that you require a license for commercial use.
Expand Down Expand Up @@ -531,7 +532,7 @@ __Please note: if you have setup the COSMIC database already, just extract the f
Again, replace _*DATABASEFOLDER*_ with your absolute path.

```bash
docker run --rm -v *DATABASEFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/database -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -v *DATABASEFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/database -p 80:8000 boutroslab/crispranalyzer:latest
```


Expand Down Expand Up @@ -584,15 +585,17 @@ In order to use these files, you need to adjust the gene identifier from `Ensemb
CRISPRAnalyzeR offers pre-made sgRNA library files in FASTA format for use.
You can use them along with your read count (please see the format) or raw NGS sequencing files (.fastq.fz).

__All pre-made libraries can be found [here](https://github.com/boutroslab/CRISPRAnalyzeR/tree/master/fasta)__


|Library Name | Lab | Pubmed ID | Addgene | Download |
|-------------|-----|-----------|---------|----------|
|CLD Benchmarking | Boutros | 27013184 | NA | [FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_CLD_library.fasta) |
|CLD Benchmarking | Boutros | 27013184 | NA | [FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/pilotscreen.fasta) |
|Gecko V2 | Zhang | 25075903 | [here](https://www.addgene.org/crispr/libraries/geckov2/) | [A+B FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_GeckoV2_all.fasta) [A FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_GeckoV2_HGLib_A.fasta) [B FASTA](https://github.com/boutroslab/crispr-analyzer/tree/master/fasta/FASTA_GeckoV2_HGLib_B.fasta) |
|Gecko V2 MOUSE| Zhang | 25075903 | [here](https://www.addgene.org/pooled-library/zhang-mouse-gecko-v2/) | [A FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_GeckoV2_MGLib_A.fasta) [B FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_GeckoV2_MGLib_B.fasta) |
|Gecko V2 MOUSE| Zhang | 25075903 | [here](https://www.addgene.org/pooled-library/zhang-mouse-gecko-v2/) | [A FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_GeckoV2_Mouse_A.fasta) [B FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_GeckoV2_Mouse_B.fasta) |
|Torronto KnockOut Library (TKOv1) | Moffat | 26627737 | [here](https://www.addgene.org/pooled-library/moffat-crispr-knockout/) | [90K FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_TKO_90K_library.fasta) & [85K FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_TKO_85Ksupp_library.fasta) |
|Brunello | Doench | 26780180 | [here](https://www.addgene.org/pooled-library/broadgpp-crispr-knockout/) | [FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_brunello_library.fasta) |
|CRISPRa / CRISPRi | Weissmann | 25307932 | [here](https://www.addgene.org/crispr/libraries/) | not available yet |
|Human Lentiviral sgRNA library high cleavage activity | Sabatini | 26472758 | [here](https://www.addgene.org/crispr/libraries/) | [185K FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_Wang_v2__185K_library.fasta) |
|Brunello | Doench | 26780180 | [here](https://www.addgene.org/pooled-library/broadgpp-crispr-knockout/) | [FASTA](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_Brunello.fasta) |
|CRISPRa / CRISPRi | Weissmann | 25307932 | [here](https://www.addgene.org/crispr/libraries/) | [CRISPRa V2](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_CRISPRa_V2.fasta) [CRISPRi V2](https://rawgit.com/boutroslab/CRISPRAnalyzeR/master/fasta/FASTA_CRISPRi_V2.fasta) |
|Human Lentiviral sgRNA sub libraries | Sabatini | 24336569 | [here](https://www.addgene.org/crispr/libraries/) | not available yet |


Expand Down Expand Up @@ -699,7 +702,7 @@ _*LOGFOLDER*_ is a local folder you create to which CRISPRAnalyzeR will save and

Start CRISPRAnalyzeR using the `-v` command, e.g.
```bash
docker run --rm -v *LOGFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/log -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm -v *LOGFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/log -p 80:8000 boutroslab/crispranalyzer:latest
```
# Increasing the core ulimit

Expand All @@ -708,7 +711,7 @@ For some genome-wide screens, CRISPRAnalyzeR can abort the report generation due
For 8 GB of the so called `c stack space`, you need to set the value of 8GB in Kb - 8.589.934.592 with `--ulimit stack=8589934592:8589934592`.

```bash
docker run --rm --ulimit stack=8589934592:8589934592 -v *LOGFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/log -p 80:3838 boutroslab/crispranalyzer:latest
docker run --rm --ulimit stack=8589934592:8589934592 -v *LOGFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/log -p 80:8000 boutroslab/crispranalyzer:latest
```


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