Forum:How to get native bash in Windows 10

Question

[Antonio R. Franco]

The Windows 10 anniversary update that allow the installation of native Ubuntu bash Linux into Windows 10 is available

This link shows how to get this update

And this one explain the way to install this bash shell

This is a direct link to get the update file

[Istvan Albert]

Weirdly enough fastqc will not work on Bash for Windows - and it fails in very mysterious way.

It will stop after reporting the file as being 100% done, will hang for many minutes than crash out with:

 A fatal error has been detected by the Java Runtime Environment:

[Antonio R. Franco]

I did not have the same problem. After running the command fastqc my_fastq_file, the systems hangs up and does not provide any output. FastQC is well installed, as the fastqc --help command works

I installed the latest java SRE and the default settings, so I have not a clue

[Antonio R. Franco]

I've been looking for some help, and I was recommended to use the strace command to try to debug the problem or to get further information

$ strace -o output_information_file <command>

Answer 1

[EagleEye]

Is this a bioinformatics question?

Anyway, my suggestion is instead of going for any tweaks, wait for Windows 10 Anniversary Update and follow the instructions as you mentioned in second link. I will not recommend to download the update file yourself and run, since the file has some problems. Update using update center from Windows, if you see the it is available for your PC.

[Antonio R. Franco]

For now, it seems that you need to look for the Anniversary update if you want it to be installed on your PC if you are not a member of the Microsoft development program.

In my opinion, the problems you have mentioned are usual problems that affect to any kind of update, and solutions (not required in my case) are provided. Windows 10 and bash are working very well on my computer

Answer 2

[Antonio R. Franco]

I installed the Ubuntu bash into Windows 10 seamless and without any problems

Then I decided to install kallisto to try

It required the installation of cmake, the zlib and some accessories libraries. It was needed the installation of g++ as well, but since apt-get is implemented, that was an easy task.

Kallisto was compiled from source and is now working properly on my PC. I used the fasta test files provided and everything seems to be going terrific

[dally]

My question is, how do you find the path where your bash stores files? Does everything have to be moved using the command line or can you use the File Explorer to move files in and out?

[Antonio R. Franco]

You can find files in any fixed or removable disks/memory within the bash window by accessing to the /mnt directory from the command line. All disks are mounted by default and are named as usual as /mnt/c /mnt/d, etc.

Taken from the web page Remember, software you install in the Bash shell is restricted to the Bash shell. You can’t access it from the Command Prompt, PowerShell, or elsewhere in Windows. Software in the Bash shell also can’t interact directly with or launch Windows programs, although the Bash environment and Windows have access to the same files on your computer.

Does this answer your question ?