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hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course
https://www.singlecellcourse.org
GNU General Public License v3.0
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"trim_galore" command could not be found #166

Closed zzygyx9119 closed 4 years ago

zzygyx9119 commented 4 years ago

I am trying to follow the tutorials in RStudio. In "process-raw-QC.Rmd", when I run the following command, it said that trim_galore could not be found. I redownloaded the image, but still got the problem. Could you please let me know how to solve this? Should I try earlier version of this class? Thank you!

`

trim_galore -h

`

/tmp/RtmpgcO0S6/chunk-code-2e2786f67e.txt: line 1: trim_galore: command not found

Jeff

zzygyx9119 commented 4 years ago

Sorry, I forgot to mention that I am using the latest version v4.11.

zzygyx9119 commented 4 years ago

I solved this issue. Basically, go to folder /usr/local/bin, recreate the link "sudo ln -s /opt/TrimGalore/TrimGalore-0.4.5/trim_galore ." . Hopefully this is helpful to others.

Jeff

zcle commented 3 years ago

Hi, I also encounter the same question. While I am using the windows platform. Do you have any suggestions for this? Thanks!

zcle commented 3 years ago

Did something similar to what zzygyx9119 mentioned, I also solved the issue. Since I use docker in Windows, I open the docker CLI (something like terminal), and I go to folder /usr/local/bin, delete trim_galore and then recreate the link by "sudo ln -s /opt/TrimGalore/TrimGalore-0.4.5/trim_galore trim_galore". Then it is ok