Error, cannot locate STAR program in the PATH setting at ./STAR-Fusion line 463.

[jdjdj0202]

Hi,
I am trying to run STAR-Fusion.

My command was as follows:

ubuntu@ip-ooo-oo-oo-oo:~/STAR-Fusion-v1.12.0$ ./STAR-Fusion \ --left_fq home/ubuntu/RNA/ATL005_R1_fastq.gz \ --right_fq home/ubuntu/RNA/ATL005_R2_fastq.gz \ --genome_lib_dir .//home/ubuntu/trinityrnaseq-v2.15.1/GRCh38_gencode_v37_CTAT_lib_Mar012021.source.tar.gz

I got error message:
Error, cannot locate STAR program in the PATH setting at ./STAR-Fusion line 463.

I run this command line at STAR-Fusion-v1.12.0.
Is it related with environment path?
Because I am not familiar with linux, I did not set any environment path and used absolute path as possible.

Please help me.
Thanks a lot.

[brianjohnhaas]

Hi, To avoid installation issues, I'd suggest using our singularity image if possible: https://github.com/STAR-Fusion/STAR-Fusion/wiki#want-to-use-singularity otherwise, you'd need to install STAR and other software modules: https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion best, ~b

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On Fri, Sep 1, 2023 at 1:16 PM jdjdj0202 ***@***.***> wrote: Hi, I am trying to run STAR-Fusion. My command was as follows: ***@***.***:~/STAR-Fusion-v1.12.0$ ./STAR-Fusion \ --left_fq home/ubuntu/RNA/ATL005_R1_fastq.gz \ --right_fq home/ubuntu/RNA/ATL005_R2_fastq.gz \ --genome_lib_dir .//home/ubuntu/trinityrnaseq-v2.15.1/GRCh38_gencode_v37_CTAT_lib_Mar012021.source.tar.gz I got error message: Error, cannot locate STAR program in the PATH setting at ./STAR-Fusion line 463. I run this command line at STAR-Fusion-v1.12.0. Is it related with environment path? Because I am not familiar with linux, I did not set any environment path and used absolute path as possible. Please help me. Thanks a lot. — Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX4KWZ3KGQRH3LXMWIDXYG7XNANCNFSM6AAAAAA4HNHXFQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[brianjohnhaas]

Hi, Instead of conda, can you give our singularity image a try? https://github.com/STAR-Fusion/STAR-Fusion/wiki#want-to-use-singularity I support the singularity and docker images, but I'm not responsible for the conda installations. best, ~b

…

On Thu, Oct 12, 2023 at 11:28 PM jdjdj0202 ***@***.***> wrote: Thank you for your reply. I think I installed STAR-FUSION. It seems to a problem of *running the program* in terminal. I searched similar issues on Google. Some people left comments on path setting. When I run ./.zshrc, I found the below: >>> conda initialize >>> !! Contents within this block are managed by 'conda init' !! __conda_setup="$('/Users/dajeong/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/Users/dajeong/anaconda3/etc/profile.d/conda.sh" ]; then . "/Users/dajeong/anaconda3/etc/profile.d/conda.sh" else export PATH="/Users/dajeong/anaconda3/bin:$PATH" fi fi unset __conda_setup <<< conda initialize <<< How would I edit this? .. Thanks. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX2IXMC6MCVSBFMVPB3X7CYNJANCNFSM6AAAAAA4HNHXFQ> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>