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LEARNING MATERIALS
 

 

 

 

 

 

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Step 3Before you start using the rnaQUAST 1.1.0, you need to make sure that the following softwares are added to your PATH

Code Block
$ export PATH=/opt/rnaQUAST-1.1.0/ncbi-blast-2.3.0+/bin/:$PATH
$ export PATH=/opt/rnaQUAST-1.1.0/blat/:$PATH
$ export PATH=/opt/rnaQUAST-1.1.0/BUSCO_v1.1b1/:$PATH
$ export PATH=/opt/rnaQUAST-1.1.0/GeneMarkS-T/:$PATH
$ export PATH=/opt/rnaQUAST-1.1.0/STAR-2.5.1b/bin/Linux_x86_64_static/:$PATH
$ export PATH=/opt/rnaQUAST-1.1.0/tophat-2.1.0.Linux_x86_64/:$PATH
$ export PATH=/opt/rnaQUAST-1.1.0/bowtie2-2.2.7/:$PATH 

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Step 5. Set up a rnaQUAST 1.1.0 test run to check that everything is installed correctly and all the software are added to the $PATH environmental variable
Info

It is recommended to redirect the output to home directory because of the disk space restrictions on /opt directory

 

Code Block
languagebash
$ python rnaQUAST.py --test

Basic run:

Info

It is recommended to redirect the output to home directory because of the disk space restrictions on /opt directory

Info

By default, the

above test run

rnaQUAST 1.1.0 uses GMAP

for running rnaQUAST

. If you want to run the above test using BLAT

, you should run like this

option.

 

a. Using rnaQUAST 1.1.0 tool using GMAP  (default)

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Info
titleOutputs

For detailed explanation of the outputs with each of the above runs, please refer to rnaQUAST 1.1.0 manual