"app_gawk" was asked, but not found

[aseedb]

Hi, I specified the path of gawk in settings. Yet when I run a process on an image I get this error message in the console: Initializing: "auto -> 0000000002" "app_gawk" was asked, but not found "realcell" was asked, but not found "realang" was asked, but not found

I have compiled and installed focus in an anaconda environment. Any idea on what could be wrong?

Benoit Z

[rdrighetto]

Hi Benoit,

Did the scripts you run finished successfully?

Sometimes FOCUS can give these error messages in the console even though everything is fine. I'm not sure yet why it does that. If there are problems in running the scripts, please let us know so we can investigate it further.

-- Ricardo Diogo Righetto

2017-11-29 16:05 GMT+01:00 aseedb notifications@github.com:

Hi, I specified the path of gawk in settings. Yet when I run a process on an image I get this error message in the console: Initializing: "auto -> 0000000002" "app_gawk" was asked, but not found "realcell" was asked, but not found "realang" was asked, but not found

I have compiled and installed focus in an anaconda environment. Any idea on what could be wrong?

Benoit Z

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[aseedb]

Hi Ricardo, Nothing is running (top shows no activity). Focus gui acts as if the job was running though (can’t close the tab without clicking stop)

[rdrighetto]

Hi Benoit,

I mentioned that, because it can be that the messages in the console have nothing to do with the actual problem. Which script did you try to run? Does it work if you try to run other scripts or is it always the same error?

-- Ricardo Diogo Righetto

2017-11-29 17:51 GMT+01:00 aseedb notifications@github.com:

Hi Ricardo, Nothing is running (top shows no activity). Focus gui acts as if the job was running though (can’t close the tab without clicking stop)

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[aseedb]

Hi Ricardo, I was trying to run Align w/ Zorro. Tried as well align with unblur and with motioncor2, gctf, ctffind4.1, measure iciness. With all of them I get the same behaviour, i.e. nothing happening. Interestingly I have not installed ctffind and when I click start there is no error message (apart from the console output). I guess it means that the process stops pretty early on.

[sthennin]

Hi Benoit, the "app_gawk not found" and "app_python not found" errors were not important. These two variables should not be set by a script. The variables defined in the "SETTINGS" panel are defined system-wide. They are not listed in the project-wide database, nor the image-specific database. Therefore, when the old script tried to define them with "set app_gawk = "" ", then the error message was printed, because these variables weren't found in the project-wide or image-specific databases. I have now removed these two definitions from the scripts, so that the annoying error messages should not longer appear.

Other than that, it looks as if your scripts aren't starting at all. Are you sure you have TCSH installed on your system? Maybe, FOCUS is trying to start a TCSH script, but that shell isn't even there?

Henning.

[aseedb]

Hi Henning, Thanks for your message. That must definitely be the problem. I am 99% sure tcsh is not installed. I’ll report back when I can test this (most likely next week). I also have another question (maybe I should open a new issue). How do you get focus and eman2.2 to coexist happily? Eman requires qt 4 while focus requires qt 5. One way would be to compile and install eman in a separate anaconda environment than focus but then can you specify that all focus scripts calling eman must activate eman environment?

[rdrighetto]

@Henning: Thanks for resolving that misleading error messages, and indeed seems to be a case of missing tcsh.

@Benoit: Yes, that is the way to go with EMAN2. The FOCUS initialization scripts will take care of setting up the environments properly, just make sure you specify the EMAN2 installation directory in the Settings. Also, FOCUS should need the Qt5 libraries only for building, so you can actually have your EMAN2 environment set up by default and only load Qt5 when you build FOCUS - that's usually how I do via a modules system (or sourcing scripts).

-- Ricardo Diogo Righetto

2017-11-30 17:55 GMT+01:00 aseedb notifications@github.com:

Hi Henning, Thanks for your message. That must definitely be the problem. I am 99% sure tcsh is not installed. I’ll report back when I can test this (most likely next week). I also have another question (maybe I should open a new issue). How do you get focus and eman2.2 to coexist happily? Eman requires qt 4 while focus requires qt 5. One way would be to compile and install eman in a separate anaconda environment than focus but then can you specify that all focus scripts calling eman must activate eman environment?

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[henning]

No idea what you talk about

Henning

Ricardo Righetto notifications@github.com schrieb am Do. 30. Nov. 2017 um 18:14:

@Henning: Thanks for resolving that misleading error messages, and indeed seems to be a case of missing tcsh.

@Benoit: Yes, that is the way to go with EMAN2. The FOCUS initialization scripts will take care of setting up the environments properly, just make sure you specify the EMAN2 installation directory in the Settings. Also, FOCUS should need the Qt5 libraries only for building, so you can actually have your EMAN2 environment set up by default and only load Qt5 when you build FOCUS - that's usually how I do via a modules system (or sourcing scripts).

-- Ricardo Diogo Righetto

2017-11-30 17:55 GMT+01:00 aseedb notifications@github.com:

Hi Henning, Thanks for your message. That must definitely be the problem. I am 99% sure tcsh is not installed. I’ll report back when I can test this (most likely next week). I also have another question (maybe I should open a new issue). How do you get focus and eman2.2 to coexist happily? Eman requires qt 4 while focus requires qt 5. One way would be to compile and install eman in a separate anaconda environment than focus but then can you specify that all focus scripts calling eman must activate eman environment?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/C-CINA/focus/issues/204#issuecomment-348250857, or mute the thread < https://github.com/notifications/unsubscribe-auth/AHVvf7XEj7UAR32rPJuN70oiUGl8EvbHks5s7t38gaJpZM4QvG7q

.

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-- Henning Sprang http://www.sprang.de

[rdrighetto]

Sorry, didn't realize that Github would actually tag the wrong Henning and the wrong Benoit :-)

-- Ricardo Diogo Righetto

2017-11-30 19:22 GMT+01:00 Henning Sprang notifications@github.com:

No idea what you talk about

Henning

Ricardo Righetto notifications@github.com schrieb am Do. 30. Nov. 2017 um 18:14:

@Henning: Thanks for resolving that misleading error messages, and indeed seems to be a case of missing tcsh.

@Benoit: Yes, that is the way to go with EMAN2. The FOCUS initialization scripts will take care of setting up the environments properly, just make sure you specify the EMAN2 installation directory in the Settings. Also, FOCUS should need the Qt5 libraries only for building, so you can actually have your EMAN2 environment set up by default and only load Qt5 when you build FOCUS - that's usually how I do via a modules system (or sourcing scripts).

-- Ricardo Diogo Righetto

2017-11-30 17:55 GMT+01:00 aseedb notifications@github.com:

Hi Henning, Thanks for your message. That must definitely be the problem. I am 99% sure tcsh is not installed. I’ll report back when I can test this (most likely next week). I also have another question (maybe I should open a new issue). How do you get focus and eman2.2 to coexist happily? Eman requires qt 4 while focus requires qt 5. One way would be to compile and install eman in a separate anaconda environment than focus but then can you specify that all focus scripts calling eman must activate eman environment?

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.

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-- Henning Sprang http://www.sprang.de

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[henning]

Ah i see... yes it notifies people with matching usernames - and we were early account creators obviously 😉

Ricardo Righetto notifications@github.com schrieb am Do. 30. Nov. 2017 um 18:28:

Sorry, didn't realize that Github would actually tag the wrong Henning and the wrong Benoit :-)

-- Ricardo Diogo Righetto

2017-11-30 19:22 GMT+01:00 Henning Sprang notifications@github.com:

No idea what you talk about

Henning

Ricardo Righetto notifications@github.com schrieb am Do. 30. Nov. 2017 um 18:14:

@Henning: Thanks for resolving that misleading error messages, and indeed seems to be a case of missing tcsh.

@Benoit: Yes, that is the way to go with EMAN2. The FOCUS initialization scripts will take care of setting up the environments properly, just make sure you specify the EMAN2 installation directory in the Settings. Also, FOCUS should need the Qt5 libraries only for building, so you can actually have your EMAN2 environment set up by default and only load Qt5 when you build FOCUS - that's usually how I do via a modules system (or sourcing scripts).

-- Ricardo Diogo Righetto

2017-11-30 17:55 GMT+01:00 aseedb notifications@github.com:

Hi Henning, Thanks for your message. That must definitely be the problem. I am 99% sure tcsh is not installed. I’ll report back when I can test this (most likely next week). I also have another question (maybe I should open a new issue). How do you get focus and eman2.2 to coexist happily? Eman requires qt 4 while focus requires qt 5. One way would be to compile and install eman in a separate anaconda environment than focus but then can you specify that all focus scripts calling eman must activate eman environment?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/C-CINA/focus/issues/204#issuecomment-348250857, or mute the thread < https://github.com/notifications/unsubscribe-auth/ AHVvf7XEj7UAR32rPJuN70oiUGl8EvbHks5s7t38gaJpZM4QvG7q

.

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-- Henning Sprang http://www.sprang.de

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.

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-- Henning Sprang http://www.sprang.de

[aseedb]

:-) OK sounds good Ricardo. Thanks for the details.

[aseedb]

Installing tcsh indeed resolved the issue. Thanks