--stranded_mode RF

[sanhe374]

When including the --stranded_mode RF in my telescope pipeline I get the following error:

telescope: error: unrecognized arguments: --stranded_mode RF

I am using Telescope version 1.0.3

Is there a solution to this problem. Telescope runs if I remove the --stranded_mode option.

[sanhe374]

@mlbendall and @mgreenig Do you have any solutions to the stranded_mode that seems to be unrecognized in Telescope?

[maxfieldk]

@sanhe374 Hi, I've had the same issue and after quite a bit of messing about got it to work.
You will have to install telescope from the sc_remove branch (I noticed it was ahead of main in terms of commits).
You can do so as follows:
mamba env create -n telescope https://github.com/mlbendall/telescope/raw/main/environment.yml
conda activate telescope
pip install git+https://github.com/mlbendall/telescope.git@sc_remove
telescope --version
Best of luck!

[mgreenig]

Hi @sanhe374 @maxfieldk, apologies for the lack of response, I pushed a fix when I saw this issue but forgot to reply to this thread. Indeed the sc_remove branch contains the updated version where the new argument should be accepted. Basic tests for that branch have passed on my machine but we are waiting to consolidate some new changes and do more testing before merging into main. However for now sc_remove should be fine as @maxfieldk noted.

[SiLu72]

Hi, I am definitely not familiar with conda environments. Having said this, I am trying to follow the instructions in the github page to have the latest version of telescope installed (I ame interested in the stranded option). However I get this error. Can somone help solve it? Thanks
mamba env create -n telescope https://github.com/mlbendall/telescope/raw/main/environment.yml
bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.

warning libmamba Please make sure you understand Anaconda Terms of Services.

warning libmamba See: https://legal.anaconda.com/policies/en/

error libmamba Could not solve for environment specs
The following package could not be installed
└─ //github.com/mlbendall/telescope/raw/main/environment.yml =* * does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs