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

[Pablo C. <pc...@cn...>]

Dear Somnath!


I guess you've run literally what Jose said:


scipion "xmipp_***"


Quite often, *** means "any word or characters".


just replace the 3 * with the xmipp progam you want to run.


For your initial query:

*scipion xmipp_**image_align*

But bear in mind that any other xmipp program could be executed the same 
way, thus the generic, literally useless, "xmipp_***".


On 05/12/17 16:36, Somnath Dutta wrote:
>
> 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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