Installation Issue

[chandramisra]

Hi

I am trying to install SUPPA2 in ubuntu in Windows. The installation is complete but I cant find the suppa.py executable file. I dont know what is the issue. I tried both conda install and pip install SUPPA==2.3 but its not working. Can you please help me.

Thanks for the help.

[EduEyras]

Hi,

were you able to find where suppa.py is? Maybe JC or Miha can help you with the Windows installation

Best

Eduardo

On Thu, 16 Apr 2020 at 13:17, namansep [email protected] wrote:

Hi

I am trying to install SUPPA2 in ubuntu in Windows. The installation is complete but I cant find the suppa.py executable file. I dont know what is the issue. I tried both conda install and pip install SUPPA==2.3 but its not working. Can you please help me.

Thanks for the help.

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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[chandramisra]

Hi

Thanks for the reply. The problem still persist. Do you know how can i reach them?

Thanks Chandra

[linagapa]

Hi Eduardo,

I'm having the same issue. I tried with conda install and pip3 install SUPPA==2.3 and in both cases there was a folder created with the name SUPPA-2.3-py3.7.egg-info in my python3.7/site-packages folder but without any executable files, just these ones: dependency_links.txt PKG-INFO requires.txt SOURCES.txt top_level.txt

Could the executables be located somewhere else?

Thanks a lot in advance for any help on this.

Lina.

[EduEyras]

Hi Lina,

thanks for your message. The pip install is probably not up-to-date. If you clone or download the latest version of the software it should work fine Sorry about that. E.

On Fri, 5 Mar 2021 at 02:04, linagapa [email protected] wrote:

Hi Eduardo,

I'm having the same issue. I tried with conda install and pip3 install SUPPA==2.3 and in both cases there was a folder created with the name SUPPA-2.3-py3.7.egg-info in my python3.7/site-packages folder but without any executable files, just these ones: dependency_links.txt PKG-INFO requires.txt SOURCES.txt top_level.txt

Could the executables be located somewhere else?

Thanks a lot in advance for any help on this.

Lina.

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[linagapa]

Hi Eduardo,

Yes, cloning the latest version works indeed. Thanks a lot.

Lina.

[sxs1647]

Hi Eduardo and Lina,

I am also experiencing the same issue that cannot find the "suppy.py" file after using "pip install SUPPA==2.3" on the server of our university. So, I cloned the latest version. I would like to know what I should do after getting the clone. I use the server of our university and the clone is in my file on the server. I used the following command in bash:

~/SUPPA/suppa.py generateEvents -i Homo_sapiens.GRCh38.103.gtf -o tEvents -f -ioe

But it shows "Permission denied". I would like to know if I should do something else before directly using the "suppy.py" file on the server? And I also would like to know more about the details on how you solved this issue and get SUPPA work after cloning the latest version.

Thank you so much for your help! ^_^

best, Shenyu

[EduEyras]

Hi,

Have you tried running the command with a python call?

python3.4 ~/SUPPA/suppa.py generateEvents -i Homo_sapiens.GRCh38.103.gtf -o tEvents -f -ioe

It should work as long as the server allows you to run Python scripts.

E.

On Wed, 17 Mar 2021 at 17:04, sxs1647 @.***> wrote:

Hi Eduardo and Lina,

I am also experiencing the same issue that cannot find the "suppy.py" file after using "pip install SUPPA==2.3" on the server of our university. So, I cloned the latest version. I would like to know what I should do after getting the clone. I use the server of our university and the clone is in my file on the server. I used the following command in bash:

~/SUPPA/suppa.py generateEvents -i Homo_sapiens.GRCh38.103.gtf -o tEvents -f -ioe

But it shows "Permission denied". I would like to know if I should do something else before directly using the "suppy.py" file on the server? And I also would like to know more about the details on how you solved this issue and get SUPPA work after cloning the latest version.

Thank you so much for your help! ^_^

best, Shenyu

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[sxs1647]

Hi Eduardo,

That works well for me now! I use:

!python ~/SUPPA/suppa.py generateEvents -i Homo_sapiens.GRCh38.103.gtf -o tEvents -f -ioi

in python and it works!

And in bash, I use:

python ~/SUPPA/suppa.py generateEvents -i Homo_sapiens.GRCh38.103.gtf -o tEvents -f -ioi

and it shows:

import pandas as pd ImportError: No module named pandas

It seems like the python modules cannot be detected in the file. I am ok with it. I can use python to run the command.

Thank you so much for your precious direction! ^_^

best, Shenyu