Re: [scipion-users] Scipion xmipp file not found

[Somnath D. <so...@ii...>]

Hi Jose,


Thank you for your help and quick reply. I am following your suggestions.

scipion e2projectmanager.py is working fine.


[somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/scipion e2projectmanager.py


Scipion v1.1 (2017-06-14) Balbino


>>>>> python  /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py "e2projectmanager.py"

** Running command: e2projectmanager.py


But scipion xmipp_*** is showing the following error


[somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/scipion xmipp_***


Scipion v1.1 (2017-06-14) Balbino


>>>>> python  /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py "xmipp_***"

** Running command: xmipp_***

/bin/sh: xmipp_***: command not found

Traceback (most recent call last):

  File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py", line 41, in <module>

    runProgram(program, params)

  File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/em/__init__.py", line 185, in runProgram

    pwutils.runJob(None, program, params, env=env)

  File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/utils/process.py", line 51, in runJob

    return runCommand(command, env, cwd)

  File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/utils/process.py", line 65, in runCommand

    check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, env=env, cwd=cwd)

  File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/lib/python2.7/subprocess.py", line 540, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'xmipp_*** ' returned non-zero exit status 127


can you please help me to resolve this problem?  I mentioned in my previous email that xmipp was working fine and opening when I used the same terminal to install the Scipion program.


Thanks,


Best,

Somnath


________________________________
From: Jose Miguel de la Rosa Trevin <del...@gm...>
Sent: 05 December 2017 15:39:06
To: Somnath Dutta
Cc: sci...@li...
Subject: Re: [scipion-users] Scipion xmipp file not found

Hi Somnath,

Scipion try to avoid that users need to modify their environment...so the path and other
variables are set when you open Scipion.

So, for easily open any other EM package, you can do it like:

scipion xmipp_***
scipion e2projectmanager.py
scipion relion_***

And so forth.

Best,
Jose Miguel


On Tue, Dec 5, 2017 at 10:25 AM, Somnath Dutta <so...@ii...<mailto:so...@ii...>> wrote:

Hi,


I have installed Scipion. After finishing my installation, when I am using the same terminal to open xmipp or eman, I can open it. But whenever I am using a new terminal to run any GUI, like xmipp, e2projectmanager.py , I can't open any of these programs. It is showing the following errors:


[somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align

/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align: error while loading shared libraries: libXmippAlglib.so: cannot open shared object file: No such file or directory


How Can I resolve this problem? Thanks in advance.


Thanks


Best,

Somnath



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