<p>Chromosomer only exists for Python 2. You should thus be able to install it via</p>

<pre><code>pip2 install chromosomer
</code></pre>

<hr>

<p><strong>But:</strong></p>

<p>Your Python installation is a bit screwed up: there are Python 2 and Python 3, which are unfortunately incompatible.</p>

<p>On your system <code>python</code> and <code>pip</code> seem to be aliases for Python 3, which I’d strongly recommend against (lots of tools will break). Instead, they should alias Python 2. Python 3 should be invoked via <code>python3</code>/<code>pip3</code>.</p>

CC BY-SA 3.0
2017-08-09T16:42:03.553Z
That's a pretty sweeping statement. The command `python` defaults to python3 on my two Arch systems and various Ubuntu boxes we use at work and I've never had issues with it. What makes you say that using python2 as the default is better? And on what systems?
terdon
CC BY-SA 3.0
2017-08-09T17:02:38.797Z
@terdon It's from a PEP recommendation. And failing to do so, while not catastrophic, definitely breaks many scripts that assume `python` = Python 2. Not a fan of Arch's/Ubuntu's decision to ignore that unnecessarily.
Konrad Rudolph
CC BY-SA 3.0
2017-08-09T17:31:22.127Z
Well, I'd argue that using a shebang line calling `python` instead of `python[23]` is a very bad design decision since the python devs, in their infinite wisdom, made the two versions incompatible. Either way, your advice is dangerous since, presumably, the OP has a working system with python3 as the default and changing that will break lots of tools while leaving it as is will not.
terdon
CC BY-SA 3.0
2017-08-09T17:38:46.407Z
@terdon You realise that there are Python scripts that predate the existence of Python 3, right? The all will, by necessity, have `python` in their shebang line. And fixing the system shouldn't break anything but, yes, it will require reinstalling all modules.
Konrad Rudolph
CC BY-SA 3.0
2017-08-09T16:21:04.900Z
2017-08-09T16:21:04.900Z
Konrad Rudolph
<p>I am trying to install <a href="https://github.com/gtamazian/chromosomer" rel="noreferrer">chromosomer</a> but I fail. Can anybody help me, please?</p>

<pre class="lang-none prettyprint-override"><code>$ pip install chromosomer

Collecting chromosomer
  Could not find a version that satisfies the requirement chromosomer (from versions: )
No matching distribution found for chromosomer
</code></pre>

<p>The output <code>python</code>:</p>

<pre class="lang-none prettyprint-override"><code>$ python

Python 3.6.0 |Anaconda custom (x86_64)| (default, Dec 23 2016, 13:19:00) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
</code></pre>

CC BY-SA 3.0
2017-08-09T16:26:11.793Z
The command line output from `pip` isn’t relevant for the question, I’ve thus removed. `pip --version` would have been more relevant. Also, be sure to read the [formatting help](https://bioinformatics.stackexchange.com/editing-help) for questions, especially the part about preformatted text (which applies to console output).
Konrad Rudolph
<python><software-installation>
Cannot install chromosomer
# Cannot install chromosomer

(Asked by: username_0 on 2017-08-09)

I am trying to install chromosomer but I fail. Can anybody help me, please?
$ pip install chromosomer

Collecting chromosomer
  Could not find a version that satisfies the requirement chromosomer (from versions: )
No matching distribution found for chromosomer

The output python:
$ python

Python 3.6.0 |Anaconda custom (x86_64)| (default, Dec 23 2016, 13:19:00) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

**Tags:** python, software-installation
> **Comments:**
> **username_1**: The command line output from `pip` isn’t relevant for the question, I’ve thus removed. `pip --version` would have been more relevant. Also, be sure to read the [formatting help](https://bioinformatics.stackexchange.com/editing-help) for questions, especially the part about preformatted text (which applies to console output).  

---

## 1 answers

### Answer by username_1 on 2017-08-09. Score: 6

Chromosomer only exists for Python 2. You should thus be able to install it via
pip2 install chromosomer


But:
Your Python installation is a bit screwed up: there are Python 2 and Python 3, which are unfortunately incompatible.
On your system python and pip seem to be aliases for Python 3, which I’d strongly recommend against (lots of tools will break). Instead, they should alias Python 2. Python 3 should be invoked via python3/pip3.

> **Comments:**
> **username_2**: That's a pretty sweeping statement. The command `python` defaults to python3 on my two Arch systems and various Ubuntu boxes we use at work and I've never had issues with it. What makes you say that using python2 as the default is better? And on what systems?  
> **username_1**: @terdon It's from a PEP recommendation. And failing to do so, while not catastrophic, definitely breaks many scripts that assume `python` = Python 2. Not a fan of Arch's/Ubuntu's decision to ignore that unnecessarily.  
> **username_2**: Well, I'd argue that using a shebang line calling `python` instead of `python[23]` is a very bad design decision since the python devs, in their infinite wisdom, made the two versions incompatible. Either way, your advice is dangerous since, presumably, the OP has a working system with python3 as the default and changing that will break lots of tools while leaving it as is will not.  
> **username_1**: @terdon You realise that there are Python scripts that predate the existence of Python 3, right? The all will, by necessity, have `python` in their shebang line. And fixing the system shouldn't break anything but, yes, it will require reinstalling all modules.  

---

