Install MEME-suite in cygwin

[Thi Thu Trang Phan]

Hi there,

I tried to use the command line version of MEME so trying to install cygwin in my Window 10 (64 bits).

I follow the instructions and keep getting error message (please see below)

Trang Phan@DESKTOP-OG5Q1NE /cygdrive/f/software/biology/meme-5.4.1
$ ./configure --prefix=c:/meme --enable-build-libxml2 --enable-build-libxslt
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... no
checking whether make supports nested variables... no
checking whether make supports nested variables... (cached) no
checking for gcc... no
checking for cc... no
checking for cl.exe... no
configure: error: in `/cygdrive/f/software/biology/meme-5.4.1':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details

I'm pretty new with command tools so tried to google a lot for each error. But in the end, for example the checking for gcc that got a no, I tried to install gcc in cygwin but didn't help with the error message.

Could you please suggest me how to fix these errors?

Many thanks in advance!

Best regards,

Trang

[Charles E Grant]

Hi Trang,

Given the error messages you report below, it looks like your installation of Cygwin is missing multiple programs, gcc and make among them. While we are happy to help with questions directly related to MEME, troubleshooting your installation of gcc in Cygwin is beyond the scope of help we can offer. For that sort of help you’ll need to check with your local computer support staff.

You might consider using Docker, and the MEME Suite docker container instead of Cygwin. That will avoid have to get Cygwin configured correctly. You will have to install Docker and the MEME Suite Docker container, but that is relatively straight forward. You can find information about Docker here:

https://www.docker.com/get-started/

Information about the MEME Suite Docker container is here:

https://hub.docker.com/r/memesuite/memesuite

Another alternative is to install the Windows Subsystem for Linux (https://docs.microsoft.com/en-us/windows/wsl/about) instead of Cygwin, but like Cygwin you’ll have to install and configure all the development tools in order to build the MEME Suite. However, the Windows Susbsystem for Linux is more widely used than Cygwin at this point, so it might be easier for you to find help with it.

Charles

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