2.Run¶

Note

Requirements must be installed on a computer before running the Octopus-toolkit. (Installation)

2-1.How to run the Octopus-toolkit¶

Please follow the movie clip (Youtube)

Download (Octopus-toolkit) and uncompress it to the folder where you want it to be installed.
Open the terminal application (cmd) and type the below command in
```
cd Octopus-toolkit/
java -jar Octopus-toolkit.jar
```

Or Command (Download ~ Run)

wget http://octopus-toolkit2.readthedocs.io/en/latest/_downloads/Octopus-toolkit.zip -O Octopus-toolkit.zip
unzip Octopus-toolkit.zip
cd Octopus-toolkit/
java -jar Octopus-toolkit.jar

No Java installation could be found. (Java 8 version) : (Err007-1)

No prerequisite were found. (Libraries in system) : (Err007-1)

_images/Err007_Not_Install_Libraries.png

Password for permission

_images/Err007_Complete_Installing_Requirement.png

2-2.Java Virtual Machine(VM) heap memory limited¶

Octopus-toolkit requires at least 8 Gb of the memory (32 Gb of memory for processing human/mouse RNA-seq) (Recommend : 32+ Gb RAM).

If you get errors related to running out of memory, please increase the heap memory of the Java Virtual Machine.

If your memory is less than 16Gb:

java -jar Octopus-toolkit.jar -Xms2G -Xmx16G -XX:MaxPermSize=16G -XX:PermSize=2G

Argument	Description	Recommend
`Xms`	Initial Heap Size	`2Gb`
`Xmx`	Max Heap Size	Maximum of RAM
`XX:PermSize`	Initial Permanent Size	`2Gb`
`XX:MaxPermSize`	Max Permanent Size	Maximum of RAM