Run LipidHunter using Anaconda

Please read the following instructions before you start to run LipidHunter.

Instructions

How to install Anaconda dependecies
Run LipidHunter
A step by step tutorial

How to install Anaconda dependencies

You get different program when you install Anaconda One of them is Anaconda Navigator. Locate and open the Anaconda Navigator. Anacond Navigator should lool like this:

CondaHome

From the list on the left click on the Environments.

Environment

You will need to create a new environment. In the column that you have the Search Environment box go down and click on the icon with the name Create.

The following window will be open.

createEnvironment

Put env-lipidhunter as "Environment name". Make sure the Python is checked and the default version is 2.7. As it is shown in the figure above. Then click Create.

After a few seconds you will get the following:

NewEnvironment

On the right is the list of all packages that are already installed.

There some other additional packages that the program needs.

There are the following:

  - pandas
  - scipy
  - Matplotlib
  - xlrd
  - openpyxl
  - pyside
  - ipykernel
  - pymzml
  - ipython

To install them the following steps are needed.

On the right where you see all the package go to the line on the top and select the option All for the first box. As it shows below.

Packages-line

After writing the name of the package that you want to install in the "Search Packages". In the example below, we search for pandas.

PackSearch

Click on the box corresponds to the packages that you want and then click apply.

SelectPandas

A window will be open asking if you want to proceed.

Message

Click Ok and then wait until it will be installed. After the installation of a package, the box will look like below.

InstallPanda

Then follow the same steps for all the other packages. You can add more than one packages at a time. Choose all the packages that you are interested and then click Apply. The message will show all the packages that you want to install.

MultiPack

To install pymzml package, there are different steps. As the image below click on the arrow next of the environment name. Then click on the option open a terminal.

AddPymzml

When the terminal opens click the following command:

  > pip install pymzml

Like, it is shown in the image below.

Pymzml

The installation will finish when the following the screen will look like the one below.

InstallPymzml

After you install all the packages your window should look like the following one:

PackagesView

Run LipidHunter

Spyder is another program that is downloaded with Anaconda. There different ways how to open Spyder. From Anaconda Navigator go to the Home page there you can see the following tab and click on Launch.

Spyder

Another way is to find the location of the program and double click. After starting you will get the following window.

SpyderBegin

When the Spyder opens go to the options File/Open.

File/Open

Go to the directory where you download the source code and open the LipidHunter.py

SourcePath

When you select open you will get the following window.

OpenFile

After that go to Tools/PYTHONPATHmanager.

Tools/Pythonmanager

After you click the option you will get the following window. Select + Add path.

Tools/Pythonmanager

Find the location of the environment you create. It should be inside the folder Anaconda2/envs. Choose the folder with the name that you gave.

EnvFolder

If you do not now the location you can find it from the Anaconda Navigator. If you go to the environments and choose the one you created. On the right down, you can see the path of the folder.

EnvPath

When you find it click Select Folder. The environment will be shown like below and close the window.

AddPath

Next, go to Tools/Preferences.

preference

Choose the Python Interpreter (from the list on the left) and select the option:

 Use the following Python interpreter:

On the white box write the path the python.exe file. The file is located inside the folder of the environment that you created at the beginning. If you click on the you can find the directory of the file (like the screenshot below).

python.Exe

Click Apply and then Ok.

Restart Spyder from File/Restart.

After you restart go to the window that is on the right down. There some tabs there. You can run the program from the Tab with the name Python console or IPython console.

Run using IPython console

Choose the tab with the name IPython Console. The window should look like this.

After you select the tab IPython Console, click the green Arrow from the toolbar. Or from the menu choose the option Run/Run.

The program will start running. The Ipython console should look like this.
Run using Python console.

If you choose the tab with the name Python Console. The window on the right down should look like this.

Click on the and then choose the option Run.

You will need to choose the location of the program (where you save it)

When you run the program you will get a new tab at the window on the right down.

When you start the run the following window should open.

finalOut

When you run the different options from the above window you can see that is running from the 2 consoles (Python, IPython). They will return some information for the run so you will now if there is a problem or not.

A step by step tutorial

A tutorial to use the LipidHunter will be provided soon.

Further questions?

Report your issue here: https://bitbucket.org/lpp_team/lipidhunter/issues

Wiki

LipidHunter / Run LipidHunter using Anaconda