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cihga39871 / Atria

An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
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command not found issue #8

Closed rhj1993119 closed 1 year ago

rhj1993119 commented 1 year ago

Hello, I installed Atria on Mac as guided. However, when I try to execute the command, it keeps showing command not found as below:

Last login: Wed Dec 7 09:49:48 on ttys001 (base) ryu@Ryu ~ % cd atria (base) ryu@Ryu atria % ls 2nd_2_Control_1.fastq.gz app-3.2.1 3rd_2_Control_1.fastq.gz app-3.2.1_2022-12-07T09-50 CHANGELOG.md benchmark LICENSE.md build_atria.jl Manifest.toml docs Project.toml src README.md test adapter.known.txt (base) ryu@Ryu atria % atria -h zsh: command not found: atria (base) ryu@Ryu atria %

can anybody have an idea on how to solve this? I am not familiar with programming, so I think I am missing something or may be wrong working directory?

Thanks in advance, Ryu

cihga39871 commented 1 year ago

Hi,

The quick answer is: after building atria, the binary executable Atria is available at ./app-*/bin/atria (Or somewhere in the app-3.2.1 folder). You have to link atria to one of your PATH:

sudo ln -s ./app-*/bin/atria /usr/local/bin

This should work.

Why it happened?

You have a folder named app-3.2.1, so it means you ran the build script. You typed atria -h without specify the path of atria, so your system will search atria in your environmental PATHs, and atria was not under any of PATHs. You can use echo $PATH to print your environmental paths (delimiter is :). You need to find the atria executable atria under app-3.2.1, and link it to one of your path.

cihga39871 commented 1 year ago

If the executable path of Atria is not ./app-*/bin/atria (I do not know whether the build script updated the binary path), please let me know and I will update the manual.