Scipy special fastStructure.

[auroreg...@gmail.com]

Hello,
I don't arrive to install scipy special for fastStructure. Could you explain me the method please?

[zeamne T]

Hello,

Which OS are you using?

-yc

On 17 January 2015 at 00:15, <auroreg...@gmail.com> wrote:

Hello,
I don't arrive to install scipy special for fastStructure. Could you explain me the method please?

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yujie

[auroreg...@gmail.com]

Ubuntu it's the problem?

Le samedi 17 janvier 2015 06:49:40 UTC, YC Tay a écrit :

Hello,

Which OS are you using?

-yc

On 17 January 2015 at 00:15, <auroreg...@gmail.com> wrote:

Hello,
I don't arrive to install scipy special for fastStructure. Could you explain me the method please?

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yujie

[auroreg...@gmail.com]

I had this problem :
ubuntu@ubuntu:~$ cd '/home/ubuntu/Desktop/Proj/fastStructure'
ubuntu@ubuntu:~/Desktop/Proj/fastStructure$ python structure.py
Traceback (most recent call last):
  File "structure.py", line 3, in <module>
    import fastStructure
  File "admixprop.pxd", line 5, in init fastStructure (fastStructure.c:8319)
  File "allelefreq.pxd", line 7, in init vars.admixprop (admixprop.c:5331)
  File "allelefreq.pyx", line 6, in init vars.allelefreq (allelefreq.c:7764)
ImportError: No module named scipy.special
ubuntu@ubuntu:~/Desktop/Proj/fastStructure$

Le samedi 17 janvier 2015 06:49:40 UTC, YC Tay a écrit :

Hello,

Which OS are you using?

-yc

On 17 January 2015 at 00:15, <auroreg...@gmail.com> wrote:

Hello,
I don't arrive to install scipy special for fastStructure. Could you explain me the method please?

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yujie

[zeamne T]

Hello,

The instructions are in the README file provided with fastSTRUCTURE. I just installed it on my computer yesterday, and I think by following the instructions I managed to get it:

**4. install Scipy**

    cd Downloads
    git clone http://github.com/scipy/scipy.git scipy
    cd scipy
    sudo python setup.py install
    cd ..
    sudo rm -R scipy

Did you try these?  If yes, which part were you stuck at?

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yujie

[auroreg...@gmail.com]

I dit it. All the steps before executing code are success. But when I write "python structure.py", there is this message "no module called "scipy.special". I saw in the file scipy, the file special, and i tried to install it with the same method cd downloads/cd special/sudo python setup.py install....but it didn't work, I tried to change the name special to scipy.special and its the same error.

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yujie

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yujie

[zeamne T]

Hmm I'm afraid I don't really know how to help you... I don't know if it makes a difference, but i installed these things before installing scipy (gcc, python3-zmq, python-dev), using these commands:
sudo apt-get install gcc
sudo python setup.py install
sudo apt-get install python3-zmq
sudo python setup.py install
sudo apt-get install python-dev
sudo python setup.py install

Then I installed scipy, but did not have to rename any file.

Perhaps you could do a search with the error messages to see what comes up: e.g.
http://stackoverflow.com/questions/9819733/scipy-special-import-issue

Can anybody else help?

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yujie

[Vikram Chhatre]

I agree with Yujie for the most part, except that you shouldn't need python 3.x, which is different than python 2.7.x (not just a version number difference).

Install all the dependencies as described on the github page for fastStructure and you should be good to go.  If I recall correctly, numpy and scipy are installed together.

Let us know if you run into problem.  Also, please be as detailed as possible with your questions, so that someone is able to help you quickly.

V

[auroreg...@gmail.com]

Thanks you guys, I found the problem, it was about a missing blas package. Now, fastStructure turns very well!

[xiaowei yang]

Hi, I got the same problem, do you mind telling how to solve it?

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