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Installation issue with conda #34
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Hi @Kiliankleemann, Thanks for your report! Could I ask what are the command lines you used for installing TELR? I just tried installing TELR under a new environment using mamba, the installation worked successfully. Here is the command line I used. Could you try this and let me know if this works for you? mamba create -n TELR --channel bioconda telr |
Is it a must to install with mamba? I have trouble setting up mamba. |
I installed mamba now in a new environment which I set up with CONDASUBDIR=linux-64. Then I ran
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@Kiliankleemann It seems that I can not reproduce this error by following the same steps that you used for installation, but there are two things I want to check with you to help resolve the issue.
Thanks, |
@Kiliankleemann and to this question "Is it a must to install with mamba? I have trouble setting up mamba." No, mamba is just an alternative to |
Thank you for the responses! I also tried |
I seemed to have installed telr but still get errors.
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Hi @Kiliankleemann, Thanks for the update on your installation experiment! I will look into preparing a docker container with TELR and all required dependencies built in, might give you an update over the weekend. Best, |
Hi @Kiliankleemann, I have prepared a docker container with TELR v1.1 and all its dependencies built-in. Here is an instruction on how to run TELR using this docker container. Could you please give it a try and see if it works for you? Thanks! TELR Docker ImageThis repository provides a Docker image to simplify the setup and execution of TELR without needing to deal with dependency issues. Getting Started1. Pull the Docker ImageTo use TELR via Docker, first pull the Docker image from Docker Hub: docker pull hanshunhua/telr_image:1.1 2. Run TELR using DockerGiven the various file inputs and optional arguments required by TELR, here's a general command structure to run TELR using the Docker image: docker run -v /path/to/local/data:/data hanshunhua/telr_image:1.1 /bin/bash -c "source activate TELR && telr -i /data/READS -r /data/REFERENCE -l /data/LIBRARY -o /data/OUTPUT_DIR [other options]"
Sample Command:Here is an example to run TELR through docker container using test input data available within the TELR repo. If the command works successfully, then you should expect to see the output files available under mkdir -p ~/git
cd ~/git
git clone [email protected]:bergmanlab/TELR.git
docker run -v ~/git/TELR/test:/data hanshunhua/telr_image:1.1 /bin/bash -c "source activate TELR && telr -i /data/reads.fasta -r /data/ref_38kb.fasta -l /data/library.fasta -o test_output" TELR OptionsHere's a quick overview of TELR's options:
Troubleshooting and SupportIf you encounter any issues using the TELR Docker image, please open an issue in the GitHub repository. |
I got the installation to work but also tried to docker now. Thank you so much for the efforts! I really appreciate it.
I will try on another machine. |
@Kiliankleemann thanks for helping me test this container! There are two things that might result in the permission denied error.
Regardless, good to hear that the installation is working now (I'm assuming with conda/mamba). Thanks, |
Would love to try your tool! Got this error for installation:
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