Question: Find a path to STAR
0
gravatar for sallyey2
5 months ago by
sallyey20
sallyey20 wrote:

Hi guys,

I am using a company's cluster system (SGE cluster) to run my codes & statistical programs. It's linux environment. I recently wrote a generating genome index in STAR and I was confirmed that the code should work fine, but the error file says "-bash: STAR: command not found."

Thus, I am trying to find a path to STAR so that I can specify the whole directory to STAR to run the index code, but since the cluster system is very complex and I am also new to the cluster/linux system, I am very struggling with finding a path to STAR.

Could you help me how to find the whole directory to STAR in the cluster?

Thank you very much.

rna-seq star alignment • 184 views
ADD COMMENTlink written 5 months ago by sallyey20
1

Are you sure STAR is installed on the system? Your best bet may be to ask system admins since you are not very familiar with unix/clusters. While you could use find (a unix command) you would need to know if there are certain directories where programs are generally installed (on managed systems that is very likely the case), it may be a bit complicated to use.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax89k

Thanks for your tip. I am pretty sure STAR is installed on the system since my manager is using STAR in the same cluster.. I've already asked IT team about the issue, but it usually takes a long time for me to get their response. I am not sure why my shell cannot recognize the command STAR, while my manager's does.. He has no problem using STAR for years in the same cluster.

ADD REPLYlink modified 5 months ago • written 5 months ago by sallyey20
1

Ask your manager where STAR is located then. It should then be a simple matter of using the full path to STAR or appending that location to your $PATH by using export PATH=$PATH:/path_to_STAR to make it work.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax89k
2
gravatar for Arup Ghosh
5 months ago by
Arup Ghosh2.7k
India
Arup Ghosh2.7k wrote:

Try locate -b '\STAR', if it's available in the cluster the full path will show up.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Arup Ghosh2.7k
2

Caveat: This only works if sys admins are running a process to update a database that stores this information regularly.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax89k

Neat - I did not know about this.

ADD REPLYlink written 5 months ago by Kevin Blighe65k
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