Re: [Chipster-tech] Installing Cellbender in Chipster

Sorry, the correct tools-bin version should have been chipster-4.9.0. There was one extra character 'v'.

Best regards,
Petri

----- Original Message -----
From: "chipster--- via Chipster-tech" <chi...@li...>
To: chi...@li...
Cc: "chipster" <chi...@cs...>
Sent: Thursday, 5 December, 2024 12:56:02
Subject: Re: [Chipster-tech] Installing Cellbender in Chipster

Hi Regan,

thanks for the detailed error report.

which version of the tools-bin package do you have at the moment? Our latest tools-bin version chipster-v4.9.0 (released a year ago) includes CellBender already. Would it be possible for you to download that? This would probably be the easiest solution, because then Chipster tool scripts would find the correct versions of all analysis tools in correct paths. 

If that is not an option, I can have a closer look why Chipster doesn't find your installation of the CellBender.

Best regards,
Petri

----- Original Message -----
From: "Regan Cannell via Chipster-tech" <chi...@li...>
To: chi...@li...
Cc: "Regan Cannell" <reg...@wi...>
Sent: Wednesday, 4 December, 2024 14:43:57
Subject: [Chipster-tech] Installing Cellbender in Chipster

To whom it may concern

My client has requested to use the tool called cellbender. However, this tool is not installed in the Chipster tools-bin directory, which I have mounted at /mnt/data/chipster/tools-bin/.

The documentation states that for any tool that requires R-4.2.3, we need to build the Docker image locally and then add the necessary configurations to the values.yaml file. This is what I have added to my values.yaml file:

```yaml
deployments:
 toolbox:
   password: XXXXXXXXXXXXXXXXXXXXXXXXX
   configs:
     toolbox-runtime-command-R-4.2.3-cellbender: /opt/chipster/tools/R-4.2.3/bin/R
     toolbox-runtime-image-R-4.2.3-cellbender: comp-r-4-2-3-cellbender
     toolbox-runtime-tools-bin-path-R-4.2.3-cellbender: tools-bin
```
The name of the tool in the Chipster interface is
Single-cell RNA-seq (Seurat v5, new) / Seurat v5 -Remove background contamination with CellBender,
and I've attached a screenshot of the error logs.

The logs state, "sh: 1: /opt/chipster/tools-bin/python-3.7.17/bin/cellbender: not found". My first plan of action
was to manually install the cellbender package into the tools-bin directory. I used the following script:

```bash
 wget https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tgz
 tar -xzf Python-3.7.17.tgz
 cd Python-3.7.17
 ./configure --prefix=/opt/chipster/tools-bin/python-3.7.17
 make
 make install

 /opt/chipster/tools-bin/python-3.7.17/bin/python3 --version

 cd /opt/chipster/tools-bin/python-3.7.17
 bin/pip3 install cellbender==v0.3.0
 bin/cellbender --version

```

I was able to install it, but Chipster does not recognise it.


Please assist me in figuring out what I did wrong. I'd greatly appreciate it. Thank you.

Kind regards
Regan



Mr Regan Cannell

Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB)
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