Installing EMBOSS using Cygwin64 Terminal on windows
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8.0 years ago
mossig89 ▴ 10

I'm fairly new to BioPython and wanted to use the EMBOSS needle and water tool on Windows 7 64 bit platform using Anaconda Spyder python 2.7 IDE, after adding the BioPython library in the Libs folder. To do this, I'm trying to install EMBOSS first using Cygwin 64 terminal following the instructions.

I downloaded the EMBOSS package. After uncompressing the folder and going to the directory of the uncompressed folder and performing the following command:

./configure --without-x CFLAGS=-s


I receive the following error message:

$./configure --without-x CFLAGS=-s checking for gawk... gawk checking for icc... no checking for gcc... no checking for cc... no configure: error: in /home/Khajag/EMBOSS-6.5.7/EMBOSS-6.5.7': configure: error: no acceptable C compiler found in$PATH See config.log'
for more details


What am I doing wrong here? Thanks.

alignment • 4.3k views
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8.0 years ago
hpmcwill ★ 1.2k

The error from the EMBOSS configure suggests that your Cygwin environment does not have a C compiler installed. The basic Cygwin environment does not include most of the development tools, in order to build software like EMBOSS you will need to install various additional packages, for this specific error you will need to install the Cygwin package for GCC.

You may find it easier to install the MS Windows EMBOSS package mEMBOSS, although given the current problems with the EMBOSS FTP site, it might be a little tricky to find an up to date mirror site.

For updates on the status of the EMBOSS web and FTP sites and discussion of the EMBOSS programs see the EMBOSS mailing lists.

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Thank you for this... I will try and install the cygwin package for GCC as suggested by the link provided... also I will try and find mEMBOSS and install that as well if possible, considering that the FTP site is down at the moment.

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I downloaded the GCC file namely: gcc-4.1-20080630.tar.bz2 by the link provided. After unzipping it and pasting it in the EMBOSS folder, I entered the following command again:

./configure --without-x CFLAGS=-s


this time I got the following:

$./configure --without-x CFLAGS=-s configure: warning: CFLAGS=-s: invalid host type creating cache ./config.cache checking host system type... Invalid configuration CFLAGS=-s': machine CFLAGS=' not recognized checking target system type... Invalid configuration CFLAGS=-s': machine CFLAGS=' not recognized checking build system type... Invalid configuration CFLAGS=-s': machine CFLAGS=' not recognized checking for a BSD compatible install... /usr/bin/install -c checking whether ln works... yes checking whether ln -s works... yes checking for gcc... no checking for cc... no configure: error: no acceptable cc found in$PATH


Might I ask what else is missing? Thanks.

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configure: error: no acceptable cc found in \$PATH


You still don't have GCC installed, it appears. The most foolproof method is to use the Cygwin package manager to install GCC and other developer tools. Run the Cygwin installer executable that you used to install Cygwin and select and add those packages.

I have some screenshots here that hint at the screens you should be looking at. The instructions I link to are for installing BEDOPS under Cygwin, but they should help you at least get the developer tools installed before you try to compile EMBOSS.