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I have tried to install the biopyhton on Windows 10 (using Mobaxterm), but I have not succeded.

I get the reply "bash: pip: command not found" when typing in "pip install biopython". However, when I do the same on the cmd line, there is no problem, and biopython is installed together with numpy. I use python 3.7, thus pip should be included when installating python.
Nonetheless, I have dowloaded get-pip.py and the biopython file (https://biopython.org/wiki/Download), but it didn't help. Sorry, I'm really not an experienced programmer. I think it is something regarding the path, but I just can't figure it out.

BR Jonas

Jonasml
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  • I typed it in Mobaxterm. I use windows 10. When I say "cmd line", I mean the cmd already found on the computer without using other terminals (as the one in Mobaxterm). I hope it make sense, I do not have the correct vocabularium for this. – Jonasml Jul 12 '19 at 14:51

1 Answers1

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Installing pip in MobaXTerm

  1. Install pip in MobaXTerm terminal: apt-cyg install python3-pip
  2. Upgrade pip to 19.x: pip3 install --upgrade pip
Prome
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  • Thanks for your answer. I did the first step. It took some time, but no problems occured. When I do the next step, nothing but a red x is shown. When I type in "pip install biopython"I get the same reply: "bash: pip: command not found". – Jonasml Jul 12 '19 at 12:24
  • pip3 install biopython – Prome Jul 12 '19 at 12:37
  • When I type in "pip3 install biopython" nothing but a red x is shown when it is done. Is it because the downloaded biopython zip file (from https://biopython.org/wiki/Download) should be placed in a specific folder? If so, how do you know were to place it? – Jonasml Jul 12 '19 at 13:48
  • Are you trying to install biopython on your system or inside mobaxterm terminal? The way you are describing is meant for installation directly on your sistem via CMD in windows. The error while installing biopython in mobaxterm is due to some missing dependencies. – Prome Jul 15 '19 at 05:37
  • Yes, I typed in "pip3 install biopython" in the mobaxterm terminal and got the error. I've done it on the CMD in windows, and there is no problem, I can also import Bio using python. However, I cannot do the same using mobaxterm. It says: "ImportError: No module named 'Bio'" – Jonasml Jul 16 '19 at 08:29