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Question: Install Bowtie2 on Windows 10 Home edition
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Hi All,

I am complitely new to the Bioinformatics, I am starting my PhD now and I have always been in wet lab. Nevertheless, I will work a lot with NGS experiments and I'd love to analyze my own data.

I was trying to install bowtie2 on my laptop and I am having several problems. I tried previous discussion but none of them solve mine.

My machine is a Windows 10 Home edition 64bit.

I tried to install bowtie with the source code (installed previosly MinGW-W64 and MSYS) but I got several error messages - it says my machine is not 64 bit. I modified the MakeFile with notepad. Run make and g make, nut nothing has worked. I have also tried to install Bowtie2 with mingw64.zip but also there nothing.

Does anyone have a step by step guide to help me?

Alternatively, I've installed Ubuntu on a Virtual machine and I successfully installed Bowtie2, but this is a solution that I don't like. What do you think about it?

I oculd also think to install ubuntu as a only OS, but I would prefer to have a more populaer OS because I also use different programs that don't have a ubuntu version.

ADD COMMENTlink 2.2 years ago ste.lu • 40 • updated 2.2 years ago genomax 68k
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This is anecdotal evidence but in the past I have found that Windows "home" editions are missing some system level features that result in strange messages/inability to run certain commercial bioinformatics programs (Vector NTI was one). Issues you noted with MinGW may be related to this. You should consider upgrading the home edition to pro, if you want to stick with Windows. That would allow you to install Windows subsystem for Linux (bash). Without this ability, Windows for bioinformatics analysis is going to prove limiting.

ADD REPLYlink 2.2 years ago
genomax
68k
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2

You don't need the pro edition for the Windows subsystem for Linux - I have the Home edition and it works just fine. And no, it is not Cygwin, but Microsoft's answer to Windows general command-line shoddiness. It allows you to access a Linux command-line environment directly from Windows. I've used it for many bioinformatics tasks and only had an issue with fastq-dump that has since been resolved.

You can read about how to install it here.

ADD REPLYlink 2.2 years ago
jared.andrews07
♦ 2.4k
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That is good to know. In general troubles I have seen with Windows in the past were with home edition, albeit for Win 7/8. OpenSSH is now natively available in Windows 10 (OpenSSH client/server now natively available (in beta) in Windows 10 )

ADD REPLYlink 2.2 years ago
genomax
68k
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Thanks a lot! Smoooth!!

ADD REPLYlink 2.2 years ago
ste.lu
• 40
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Thank you for your answer genomax.

"That would allow you to install Windows subsystem for Linux (bash)" Regard to this sentence, I have installed Cygwin64 terminal, is that what you meant? If so, no luck even with that one.

ADD REPLYlink 2.2 years ago
ste.lu
• 40

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