carveme_init not found

[fairquestion]

Dear author,

When I install CARVEME for windows (pip install carveme), the initialitation script carveme_init does not appear, therefore I can not try your program. Looking at your github files, carveme_init appears in your script folder. The point is that the script folder is not generated during the pip installation. What I am doing wrong? I am running python 3.6.5 with Anaconda3 These are the installed files and folders: init.py pycache config.cfg data reconstruction universe

Best, Fair

PS. framed and pandas are also not installed.

[cdanielmachado]

Using CarveMe with windows is probably not so easy. We have mainly designed and tested it using unix-like environments (linux and mac os).

I just recently realized that setuptools does not correctly create the script files in windows, mainly because they are designed to behave as bash scripts. There is a workaround for that, but we haven't implemented it yet: https://github.com/cdanielmachado/carveme/issues/24

Unfortunately, for the moment, the only option to run CarveMe on windows is to replace:

> carveme_init

and

> carve [ARGS]

With

python [anaconda folder]/Scripts/carveme_init

and

python [anaconda folder]/Scripts/carve [ARGS]

Let me know if this works.

[fairquestion]

Hi!

Thanks for your answer. Then should I directly download the files from github instead of using pip?

Best, Fair

[cdanielmachado]

The pip installer should still work fine I think. Do you get any errors during the pip installation? Can you find those files I mentioned?

[hoaltay]

Hi, For my research project, I need genome-scale models of five pathogens. I found four of them in your comprehensive embl_gems collection but only Burkholderia cenocepacia J2315 (a well-known reference strain) was missing. For this reason, I tried to build models by myself by using Carveme, but I had the aforementioned problem even I tried with the advised solution, as you may see in the attached file. I am also Windows 10 user and Anaconda or required solvers are all the latest versions. I will be really appreciated if you help me, Best, Ozlem

[cdanielmachado]

Hi @hoaltay,

It failed to run diamond because it is not in your PATH.

Make sure that you extend your PATH to include the directory where you installed the diamond executable.

You can test if diamond is in your PATH by opening a terminal and typing "diamond help".