Question: STAR - working with binary files in MacOS
0
gravatar for saraG
2.9 years ago by
saraG10
saraG10 wrote:

Hy everyone,

I would like to carry out an alternative splicing analysis of RNA-seq sata from rat (rn6). I have been trying to install STAR together with rMATS in MacOS as explained by this tutorial:

http://rnaseq-mats.sourceforge.net/user_guide.htm

However, I have had several problem with the compiler because 'clang' is not supported by openMP. I have tried to install gcc in different ways following various several forum recipes with no luck. I decided to use the 'STAR' pre-compiled MAC executable in Downloads/STAR-master/bin/MacOSX_x86_64.

https://groups.google.com/forum/#!topic/rna-star/spxOom9pcNw

They seem to run nicely. However, I got the following in the terminal: -bash: STAR: command not found I am probably doing something silly like not working in the proper directory (?) but I cannot work out my way out of here, does someone have some experience on using pre-compiled binaries to work with STAR? I would really appreciate some guidance.

rna-seq • 906 views
ADD COMMENTlink written 2.9 years ago by saraG10
1
gravatar for GenoMax
2.9 years ago by
GenoMax96k
United States
GenoMax96k wrote:

If you are in the directory with STAR executable then explicitly doing ./STAR in command or adding that directory to your $PATH are possible options. Do export PATH=$PATH:/path_to_dir_STAR_executable.

Great UNIX tutorial worth spending a few hours on.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by GenoMax96k

Hi, Using " ./STAR --runMode genomeGenerate ..." within the bin folder works. I am taking a look on the tutorial and it is very useful. Thank you so much for your help.

ADD REPLYlink written 2.9 years ago by saraG10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2237 users visited in the last hour
_