<p>I would strongly recommend to use <a href="https://bioconda.github.io/index.html" rel="nofollow noreferrer">Bioconda</a> instead of compiling. It is one of the channels ("distributors of packages") in <a href="https://anaconda.org/" rel="nofollow noreferrer">Anaconda Cloud</a> which is basically a package source for <a href="https://conda.io/docs/" rel="nofollow noreferrer">conda</a>.</p>

<p>In short - conda allows you to create virtual environments isolated from system and to install various precompiled software packages with one command (so, by the way, you can easily use multiple software versions on one system). Also, Bioconda is just one channel aiming on various bioinformatics software, but many more packages can be found in aforementioned Anaconda Cloud.</p>

<p>Tutorial how to start using Bioconda is on its homepage, and it is really easy (far more easier than to struggle with compiling).</p>

<p><a href="https://bioconda.github.io/recipes/hmmer/README.html" rel="nofollow noreferrer">Bioconda HMMER package</a></p>

<p>P.S. Of course there are cases in which you need a specific build of given software. Than it is really needed to compile manually.</p>

CC BY-SA 4.0
2018-11-16T03:53:08.303Z
Thank you. The website says "Bioconda supports only 64-bit Linux and Mac OSX." I am a Windows user, so I assume I will need to go back to compiling. Bioconda sounds amazing though; thanks for bringing it to my/our attention.
JernejT
CC BY-SA 4.0
2018-11-16T04:29:10.910Z
I tried to set up channels with `conda config --add channels defaults`, `conda config --add channels bioconda` & `conda config --add channels conda-forge` in my Anaconda prompt which seemingly worked, but `conda install hmmer` didn't.
JernejT
CC BY-SA 4.0
2018-11-16T10:54:06.870Z
@JernejT On Windows? And what does `conda install hmmer` output? Anyway, Linux is much more supported platform for bioinformatics. Worth to try :)
jirinovo
CC BY-SA 4.0
2018-11-15T12:48:25.817Z
2018-11-15T14:53:00.770Z
2018-11-15T14:53:00.770Z
jirinovo
<p>I tried to compile HMMER v3.2.1 in Cygwin using </p>

<pre><code>./configure
</code></pre>

<p>followed by </p>

<pre><code>make
</code></pre>

<p>or</p>

<pre><code>make install
</code></pre>

<p>but failed. I got this <a href="https://drive.google.com/file/d/1aMXNQOiftf09XHW8B0pXVbt-Fdk1CWtD/view" rel="nofollow noreferrer">config.log file</a> to troubleshoot and I suspect the solution is in this line: </p>

<pre><code>configure:2908: error: no acceptable C compiler found in $PATH
</code></pre>

<p>What does it mean? Is it really all I need to address? I followed the installation steps <a href="http://eddylab.org/software/hmmer/Userguide.pdf" rel="nofollow noreferrer">in this document</a>.</p>

CC BY-SA 4.0
2018-11-14T04:41:11.303Z
It means you need to download a C compiler. I would recommend using gcc!
d_kennetz
CC BY-SA 4.0
2018-11-14T05:23:47.070Z
Have a look here on how to install gcc https://askubuntu.com/questions/271388/how-to-install-gcc-4-8
Ammar Sabir Cheema
CC BY-SA 4.0
2018-11-14T05:24:08.217Z
gcc is a C compiler
Ammar Sabir Cheema
<software-installation><hmmer>
Error compiling HMMER v3.2.1
# Error compiling HMMER v3.2.1

(Asked by: username_0 on 2018-11-14)

I tried to compile HMMER v3.2.1 in Cygwin using 
./configure

followed by 
make

or
make install

but failed. I got this config.log file to troubleshoot and I suspect the solution is in this line: 
configure:2908: error: no acceptable C compiler found in $PATH

What does it mean? Is it really all I need to address? I followed the installation steps in this document.

**Tags:** software-installation, hmmer
> **Comments:**
> **username_1**: It means you need to download a C compiler. I would recommend using gcc!  
> **username_2**: Have a look here on how to install gcc https://askubuntu.com/questions/271388/how-to-install-gcc-4-8  
> **username_2**: gcc is a C compiler  

---

## 1 answers

### Answer by username_3 on 2018-11-15. Score: 3

I would strongly recommend to use [Bioconda](https://bioconda.github.io/index.html) instead of compiling. It is one of the channels ("distributors of packages") in [Anaconda Cloud](https://anaconda.org/) which is basically a package source for [conda](https://conda.io/docs/).

In short - conda allows you to create virtual environments isolated from system and to install various precompiled software packages with one command (so, by the way, you can easily use multiple software versions on one system). Also, Bioconda is just one channel aiming on various bioinformatics software, but many more packages can be found in aforementioned Anaconda Cloud.

Tutorial how to start using Bioconda is on its homepage, and it is really easy (far more easier than to struggle with compiling).

[Bioconda HMMER package](https://bioconda.github.io/recipes/hmmer/README.html)

P.S. Of course there are cases in which you need a specific build of given software. Than it is really needed to compile manually.

> **Comments:**
> **username_0**: Thank you. The website says "Bioconda supports only 64-bit Linux and Mac OSX." I am a Windows user, so I assume I will need to go back to compiling. Bioconda sounds amazing though; thanks for bringing it to my/our attention.  
> **username_0**: I tried to set up channels with `conda config --add channels defaults`, `conda config --add channels bioconda` & `conda config --add channels conda-forge` in my Anaconda prompt which seemingly worked, but `conda install hmmer` didn't.  
> **username_3**: @JernejT On Windows? And what does `conda install hmmer` output? Anyway, Linux is much more supported platform for bioinformatics. Worth to try :)  

---

