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donovan-h-parks / STAMP

Statistical Analysis of Metagenomic Profiles
GNU General Public License v3.0
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How to start STAMP from command line #27

Closed emankhalaf closed 6 years ago

emankhalaf commented 6 years ago

Hello, I am a beginner in using STAMP. I am using Ubuntu 16.04. I created an environment and installed stamp using the following code: conda install -c bioconda stamp

I have my file generated from Tax4Fun comparing reads/values of metabolic pathways in a control sample vs pathogen-treated sample. I don't know how to use stamp from the command line.

I have a previous trial where I installed the software quickly on my pc, but the test file did not work that makes me uncertain about using it based on the installation instructions.

All what I need is a good tutorial for using STAMP from command line

Thanks Eman

emankhalaf commented 6 years ago

I run: STAMP and got this error:

Traceback (most recent call last): File "/home/eman/anaconda3/envs/stamp/bin/STAMP", line 32, in from stamp import STAMP File "/home/eman/anaconda3/envs/stamp/lib/python2.7/site-packages/stamp/STAMP.py", line 38, in from stamp.GUI.plotDlg import PlotDlg # forward reference so py2app recognizes this file is required File "/home/eman/anaconda3/envs/stamp/lib/python2.7/site-packages/stamp/GUI/plotDlg.py", line 24, in from PyQt4 import QtGui, QtCore ImportError: No module named PyQt4

Actually, I have pyqt5 in the plugin folder. Does it mean I need to download pyqt4? Please help

emankhalaf commented 6 years ago

solved. Thanks

GuillaumeSwB commented 5 years ago

Hi,

Could you please tell me how did you solve it ?

NainaK6 commented 2 years ago

Hi, could anyone please let me know, how can I run STAMP from the command line in a Linux cluster?

limrp commented 1 month ago

Hi, could anyone please let me know, how can I run STAMP from the command line in a Linux cluster?

I have the same question. Does anyone has a solution for this?

emankhalaf commented 1 month ago

just type $stamp