Trouble installing SPLASH

[RebbyAnne]

I'm trying to run SPLASH on Linux. When I try the following:
curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.11.6/splash-2.11.6.linux.x64.tar.gz | tar xz cd example ./run-example.sh
The log file for the example run throws me:
/bin/sh: line 1: /usr/bin/time: No such file or directory

However. When I try:
git clone --recurse-submodules https://github.com/refresh-bio/splash cd splash make -j

I get: Error: bkc does not exist in bin nor it is installed.

I've tried separately installing the conda dependencies, but theres seems to be a SPLASH dependency on CMAKE version 3.1 which is now defunct. Any fix for this?

[marekkokot]

Hi,

Your first approach should work, so we should focus on that for now.

First thing: I realised I have not updated the docs to point to the newest version, which is v2.11.9. It's updated now, so try this again:

curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.11.9/splash-2.11.9.linux.x64.tar.gz | tar xz
cd example
./run-example.sh

Note: If you are not on linux, but for example on mac os (which is likely if you don't have /usr/bin/time), assuming ARM processor (like M1, M2, ...) replace above with:

curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.11.9/splash-2.11.9.mac.arm64.tar.gz | tar xz
cd example
./run-example.sh

If you are on Linux and there is no /usr/bin/time could you please install it? On Debian this should work

sudo apt install time

(or similar command, depending on your package manager).
After this, below command should work:

/usr/bin/time

Let me know if it helped.

Regarding bkc not found, could you give me the full output of
make -j
(on a clean repo clone)?

There is always an alternative to use docker, so you may try this.

Let me know if it helped.

[RebbyAnne]

Im on Linux. Is there an alternative to using sudo? I'm trying to install SPLASH on a shared cluster.

[marekkokot]

On cluster, I would recommend using singularity/apptainer: https://github.com/refresh-bio/SPLASH/wiki/Installation#singularity-container

is there any issue with this?

[RebbyAnne]

This works, thank you so much for the help!