Wrong download path in ngless main?

[Ulrike Löber]

Hi all,

could it be, that embl instead of GitHub path is implemented in ngless and links are not up to date anymore? Could you please check that? In General it's much more convinient now to call the latest modules, Thanks for that. Issue occured with motus 2.5

Cheers,

Ulrike

[Renato Alves]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Dear Ulrike,

If you are using:

https://github.com/ngless-toolkit/ngless-contrib/tree/master/motus.ngm/2.5

There is nothing specific about embl in this module.

If the instructions are followed the motus sofrware will be installed in the NGLESS_MODULE_DIR (usually ~/.local/share/ngless/...)

Cheers,
Renato

> --
> You received this message because you are subscribed to the Google Groups "NGLess" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ngless+un...@googlegroups.com <mailto:ngless+un...@googlegroups.com>.
> To view this discussion on the web visit https://groups.google.com/d/msgid/ngless/99daf7f6-6546-42b3-89e3-7ab7d0bfc2fc%40googlegroups.com <https://groups.google.com/d/msgid/ngless/99daf7f6-6546-42b3-89e3-7ab7d0bfc2fc%40googlegroups.com?utm_medium=email&utm_source=footer>.

- --
Renato Alves
PhD Student, Bork Group
EMBL-Heidelberg, Germany

Lab Phone: +49 6221 387 8150
Email: renato...@embl.de
orcid.org/0000-0002-7212-0234
-----BEGIN PGP SIGNATURE-----
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=Spvn
-----END PGP SIGNATURE-----

[Ulrike Löber]

Dear Renato,

Exiting after fatal error while loading and running script
System Error
Could not connect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz (got error code: 404)

is an ngless error I'm reporting.

I'm trying to set up ngless on our new centos7 vm and am struggeling with the dependencies.

Bests,

Ulrike

[Renato Alves]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Dear Ulrike,

motus 2.0 and 2.5 are not included in ngless. As such this shouldn't be happening.
It's possible that this is related to:

https://github.com/ngless-toolkit/ngless/issues/117

Could you check that motus 2.5 was manually setup as described in:

https://github.com/ngless-toolkit/ngless-contrib#install

Additionally, and guessing here, but are you missing the "local" keyword in the "import" statement.

See the example at:

https://github.com/ngless-toolkit/ngless-contrib/tree/master/motus.ngm#example

in particular the "import" section.

Cheers,
Renato

On 10/4/19 4:49 PM, 'Ulrike Löber' via NGLess wrote:
> Dear Renato,
>
> |
> Exitingafter fatal error whileloading andrunning script
> SystemError
> Couldnotconnect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz (got error code: 404)

> |
>
>
>
> is an ngless error I'm reporting.
>
> I'm trying to set up ngless on our new centos7 vm and am struggeling with the dependencies.
>
> Bests,
> Ulrike
>

> --
> You received this message because you are subscribed to the Google Groups "NGLess" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ngless+un...@googlegroups.com <mailto:ngless+un...@googlegroups.com>.

> To view this discussion on the web visit https://groups.google.com/d/msgid/ngless/675a5745-2246-4caa-9af6-25cf88390720%40googlegroups.com <https://groups.google.com/d/msgid/ngless/675a5745-2246-4caa-9af6-25cf88390720%40googlegroups.com?utm_medium=email&utm_source=footer>.

- --
Renato Alves
PhD Student, Bork Group
EMBL-Heidelberg, Germany

Lab Phone: +49 6221 387 8150
Email: renato...@embl.de
orcid.org/0000-0002-7212-0234
-----BEGIN PGP SIGNATURE-----
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=fDRh
-----END PGP SIGNATURE-----

[Ulrike Löber]

Dera Renato,

I'm trying to install ngless with latest dependencies on our new centos7 VM. So far, I was not successful

my *.ngl file:

#!/usr/bin/env ngless
ngless "1.0"
import "mocat" version "2.1.0"
import "specI" version "0.1"
local import "motus" version "2.5"
import "igc" version "0.9"
import "parallel" version "1.0"

How I installed the contributions:

./install.sh
Installing fastqp.ngm/0.3.2
Installing fastx.ngm/0.1.0
Installing metaphlan.ngm/2.0
Installing motus.ngm/2.1
Installing motus.ngm/2.5
Installing salmon.ngm/0.9.1

I did it as described and still get:

Exiting after fatal error while loading and running script
System Error

Could not connect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz (got error code: 404)

Bests,

Ulrike

[Renato Alves]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Dear Ulrike,

The error is indeed misleading. However I can only replicate it if ngless fails to find the motus 2.5 module or if it's incorrectly installed.

Can you check that the path $HOME/.local/share/ngless/data/Modules/motus.ngm/2.5 exists?

Cheers,
Renato

On 10/4/19 5:12 PM, 'Ulrike Löber' via NGLess wrote:
>
> Dera Renato,
> I'm trying to install ngless with latest dependencies on our new centos7 VM. So far, I was not successful
> my *.ngl file:
> |
> #!/usr/bin/env ngless
> ngless "1.0"
> import"mocat"version "2.1.0"
> import"specI"version "0.1"

> localimport"motus"version "2.5"

> import"igc"version "0.9"
> import"parallel"version "1.0"
> |
>
> How I installed the contributions:
>
> |
> ./install.sh
> Installingfastqp.ngm/0.3.2
> Installingfastx.ngm/0.1.0
> Installingmetaphlan.ngm/2.0
> Installingmotus.ngm/2.1
> Installingmotus.ngm/2.5
> Installingsalmon.ngm/0.9.1
>
> |
>
> I did it as described and still get:
> |

> Exitingafter fatal error whileloading andrunning script
> SystemError

> Couldnotconnect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz (got error code: 404)
> |
>
> Bests,
> Ulrike
>

> --
> You received this message because you are subscribed to the Google Groups "NGLess" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ngless+un...@googlegroups.com <mailto:ngless+un...@googlegroups.com>.

> To view this discussion on the web visit https://groups.google.com/d/msgid/ngless/8d57175d-cea8-4d5b-a4b9-7b0d53190f66%40googlegroups.com <https://groups.google.com/d/msgid/ngless/8d57175d-cea8-4d5b-a4b9-7b0d53190f66%40googlegroups.com?utm_medium=email&utm_source=footer>.

- --
Renato Alves
PhD Student, Bork Group
EMBL-Heidelberg, Germany

Lab Phone: +49 6221 387 8150
Email: renato...@embl.de
orcid.org/0000-0002-7212-0234
-----BEGIN PGP SIGNATURE-----
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=ah0b
-----END PGP SIGNATURE-----

[Ulrike Löber]

Dear Renato,

yes it exists:

ls $HOME/.local/share/ngless/data/Modules/motus.ngm/2.5
module.yaml  run.sh

Maybe I should setup ngless again. What is the suggested way to install nglessfor multiple users on centos7? May I open another thread?

Cheers,

Ulrike

[Renato Alves]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

> Maybe I should setup ngless again. What is the suggested way to install nglessfor multiple users on centos7? May I open another thread?

If ngless is installed in a shared location such as /usr/local/bin/ngless it will also look for available modules in /usr/local/share/ngless/...

However that shouldn't prevent it from finding the module in $HOME/.local/share/ngless/...

Can you provide the output of ngless --trace script.ngl ?

I don't see what might be wrong here.

Thanks,
Renato

- --
Renato Alves
PhD Student, Bork Group
EMBL-Heidelberg, Germany

Lab Phone: +49 6221 387 8150
Email: renato...@embl.de
orcid.org/0000-0002-7212-0234
-----BEGIN PGP SIGNATURE-----
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=BacZ
-----END PGP SIGNATURE-----

[Ulrike Löber]

Hi Renato,

this is the trace output:

[Tue 08-10-2019 15:29:24]: # Configuration
[Tue 08-10-2019 15:29:24]:     download base URL: https://ngless.embl.de/resources/
[Tue 08-10-2019 15:29:24]:     global data directory: /home/uloeber/anaconda3/bin/../share/ngless/data
[Tue 08-10-2019 15:29:24]:     user directory: /home/uloeber/.local/share/ngless
[Tue 08-10-2019 15:29:24]:     user data directory:  ~/.local/share/ngless/data/
[Tue 08-10-2019 15:29:24]:     temporary directory: /local/ngless-temp/
[Tue 08-10-2019 15:29:24]:     keep temporary files: False
[Tue 08-10-2019 15:29:24]:     create report: True
[Tue 08-10-2019 15:29:24]:     report directory: human-gutNEW.ngl.output_ngless
[Tue 08-10-2019 15:29:24]:     color setting: AutoColor
[Tue 08-10-2019 15:29:24]:     print header: True
[Tue 08-10-2019 15:29:24]:     subsample: False
[Tue 08-10-2019 15:29:24]:     verbosity: Normal
[Tue 08-10-2019 15:29:24]:     search path:
[Tue 08-10-2019 15:29:24]: Loading modules...
[Tue 08-10-2019 15:29:24]: Looking for module specI at `./Modules/specI.ngm/0.1/module.yaml` and did not find it.
[Tue 08-10-2019 15:29:24]: Looking for module specI at `/home/uloeber/anaconda3/bin/../share/ngless/data/Modules/specI.ngm/0.1/module.yaml` and did not find it.
[Tue 08-10-2019 15:29:24]: Looking for module specI at ` ~/.local/share/ngless/data/Modules/specI.ngm/0.1/module.yaml` and found it.
[Tue 08-10-2019 15:29:24]: Looking for module motus at `./Modules/motus.ngm/2.5/module.yaml` and did not find it.
[Tue 08-10-2019 15:29:24]: Looking for module motus at `/home/uloeber/anaconda3/bin/../share/ngless/data/Modules/motus.ngm/2.5/module.yaml` and did not find it.
[Tue 08-10-2019 15:29:24]: Looking for module motus at ` ~/.local/share/ngless/data/Modules/motus.ngm/2.5/module.yaml` and did not find it.
[Tue 08-10-2019 15:29:24]: Downloading https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz

Exiting after fatal error while loading and running script
System Error

Could not connect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz (got error code: 404)

I checked the path and the file exists.

Cheers,

Ulrike

[Renato Alves]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Hi Ulrike

> I checked the path and the file exists.

do you mean the following path?

~/.local/share/ngless/data/Modules/motus.ngm/2.5/module.yaml

If yes, there is some inconsistency in your environment.
Two possibilities come to mind.

1. Your $HOME location is not shared across machines and the modules are setup in some but not all nodes.
2. Something is modifying the $HOME or $XDG_DATA_HOME variable causing ngless to look elsewhere.
3. You have settings in $HOME/.config/ngless.conf that are overriding ngless' default behavior.

For instance, I notice that there's an extra leading space in the path printed here (just before the tilde):

Looking for module motus at ` ~/.local/share/ngless/data/Modules/motus.ngm/2.5/module.yaml`

When I run this command locally, ngless gives me `/home/ralves/.local` instead of ` ~/.local`, so I'm wondering what might be causing the difference there too.

Hope this helps.

Cheers,
Renato

On 10/8/19 3:33 PM, 'Ulrike Löber' via NGLess wrote:
> Hi Renato,
> this is the trace output:
>
> |
> [Tue08-10-201915:29:24]:# Configuration
> [Tue08-10-201915:29:24]: download baseURL:https://ngless.embl.de/resources/
> [Tue08-10-201915:29:24]: globaldata directory:/home/uloeber/anaconda3/bin/../share/ngless/data

> [Tue08-10-201915:29:24]: user directory:/home/uloeber/.local/share/ngless
> [Tue08-10-201915:29:24]: user data directory: ~/.local/share/ngless/data/
> [Tue08-10-201915:29:24]: temporary directory:/local/ngless-temp/
> [Tue08-10-201915:29:24]: keep temporary files:False
> [Tue08-10-201915:29:24]: create report:True
> [Tue08-10-201915:29:24]: report directory:human-gutNEW.ngl.output_ngless
> [Tue08-10-201915:29:24]: color setting:AutoColor

> [Tue08-10-201915:29:24]: printheader:True
> [Tue08-10-201915:29:24]: subsample:False
> [Tue08-10-201915:29:24]: verbosity:Normal
> [Tue08-10-201915:29:24]: search path:
> [Tue08-10-201915:29:24]:Loadingmodules...
> [Tue08-10-201915:29:24]:LookingformodulespecI at `./Modules/specI.ngm/0.1/module.yaml`anddid notfind it.
> [Tue08-10-201915:29:24]:LookingformodulespecI at `/home/uloeber/anaconda3/bin/../share/ngless/data/Modules/specI.ngm/0.1/module.yaml`anddid notfind it.
> [Tue08-10-201915:29:24]:LookingformodulespecI at ` ~/.local/share/ngless/data/Modules/specI.ngm/0.1/module.yaml`andfound it.
> [Tue08-10-201915:29:24]:Lookingformodulemotus at `./Modules/motus.ngm/2.5/module.yaml`anddid notfind it.
> [Tue08-10-201915:29:24]:Lookingformodulemotus at `/home/uloeber/anaconda3/bin/../share/ngless/data/Modules/motus.ngm/2.5/module.yaml`anddid notfind it.
> [Tue08-10-201915:29:24]:Lookingformodulemotus at ` ~/.local/share/ngless/data/Modules/motus.ngm/2.5/module.yaml`anddid notfind it.
> [Tue08-10-201915:29:24]:Downloadinghttps://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz

> Exitingafter fatal error whileloading andrunning script
> SystemError

> Couldnotconnect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz (got error code: 404)
>
>
> |
>
>
>
> Cheers,

> Ulrike
>
> --
> You received this message because you are subscribed to the Google Groups "NGLess" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ngless+un...@googlegroups.com <mailto:ngless+un...@googlegroups.com>.

> To view this discussion on the web visit https://groups.google.com/d/msgid/ngless/2c97c3dd-a67c-45f1-9eab-c5a5029dde3a%40googlegroups.com <https://groups.google.com/d/msgid/ngless/2c97c3dd-a67c-45f1-9eab-c5a5029dde3a%40googlegroups.com?utm_medium=email&utm_source=footer>.

- --
Renato Alves
PhD Student, Bork Group
EMBL-Heidelberg, Germany

Lab Phone: +49 6221 387 8150
Email: renato...@embl.de
orcid.org/0000-0002-7212-0234
-----BEGIN PGP SIGNATURE-----
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=Z8+n
-----END PGP SIGNATURE-----

[Ulrike Löber]

Hi Luis, hi Renato,

I gave up on this and now trying again to get the auto download to run with the mousegutprofiler. what am I doing wrong? I completely removed and reinstalled ngless. Where does this path come from and how would one change to the correct download path on github?

https://ngless.embl.de/resources/Modules/MouseGutCatalog.ngm/1.0.tar.gz

Thanks in advance,

Ulrike

(base) [uloeber@sl-sci-forsl1 Modules]$ conda install -c bioconda ngless
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/uloeber/anaconda3

  added / updated specs:
    - ngless


The following NEW packages will be INSTALLED:

  ngless             bioconda/linux-64::ngless-1.0.1-0


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(base) [uloeber@sl-sci-forsl1 Modules]$ cd /fast/AG_Forslund/Ulrike/germFreeMice/data_release/X204SC19111054-Z01-F001/raw_data/
(base) [uloeber@sl-sci-forsl1 raw_data]$ ngless --create-report --trace --temporary-directory='/fast/AG_Forslund/Ulrike/temp' mouse-gut-profiler.ngl D1 D1out
[Tue 18-02-2020 12:54:16]: # Configuration
[Tue 18-02-2020 12:54:16]:     download base URL: https://ngless.embl.de/resources/
[Tue 18-02-2020 12:54:16]:     global data directory: /home/uloeber/anaconda3/bin/../share/ngless/data
[Tue 18-02-2020 12:54:16]:     user directory: /home/uloeber/.local/share/ngless
[Tue 18-02-2020 12:54:16]:     user data directory:  ~/.local/share/ngless/data/
[Tue 18-02-2020 12:54:16]:     temporary directory: /fast/AG_Forslund/Ulrike/temp
[Tue 18-02-2020 12:54:16]:     keep temporary files: False
[Tue 18-02-2020 12:54:16]:     create report: True
[Tue 18-02-2020 12:54:16]:     report directory: mouse-gut-profiler.ngl.output_ngless
[Tue 18-02-2020 12:54:16]:     color setting: AutoColor
[Tue 18-02-2020 12:54:16]:     print header: True
[Tue 18-02-2020 12:54:16]:     subsample: False
[Tue 18-02-2020 12:54:16]:     verbosity: Normal
[Tue 18-02-2020 12:54:16]:     search path:
[Tue 18-02-2020 12:54:16]: Loading modules...
[Tue 18-02-2020 12:54:16]: Looking for module specI at `./Modules/specI.ngm/0.1/module.yaml` and did not find it.
[Tue 18-02-2020 12:54:16]: Looking for module specI at `/home/uloeber/anaconda3/bin/../share/ngless/data/Modules/specI.ngm/0.1/module.yaml` and did not find it.
[Tue 18-02-2020 12:54:16]: Looking for module specI at ` ~/.local/share/ngless/data/Modules/specI.ngm/0.1/module.yaml` and found it.
[Tue 18-02-2020 12:54:16]: Looking for module MouseGutCatalog at `./Modules/MouseGutCatalog.ngm/1.0/module.yaml` and did not find it.
[Tue 18-02-2020 12:54:16]: Looking for module MouseGutCatalog at `/home/uloeber/anaconda3/bin/../share/ngless/data/Modules/MouseGutCatalog.ngm/1.0/module.yaml` and did not find it.
[Tue 18-02-2020 12:54:16]: Looking for module MouseGutCatalog at ` ~/.local/share/ngless/data/Modules/MouseGutCatalog.ngm/1.0/module.yaml` and did not find it.
[Tue 18-02-2020 12:54:16]: Downloading https://ngless.embl.de/resources/Modules/MouseGutCatalog.ngm/1.0.tar.gz

Exiting after fatal error while loading and running script
System Error

Could not connect to https://ngless.embl.de/resources/Modules/MouseGutCatalog.ngm/1.0.tar.gz (got error code: 404)

(base) [uloeber@sl-sci-forsl1 raw_data]$ conda remove ngless
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/uloeber/anaconda3

  removed specs:
    - ngless


The following packages will be REMOVED:

  ngless-1.0.1-0


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

[Renato Alves]

Hi Ulrike,

The mouse gut profiler [1] uses MouseGutCatalog 0.9 not 1.0.

[1]
https://github.com/ngless-toolkit/ng-meta-profiler/blob/master/mouse-gut-profiler.ngl

are you by any chance using a modified version of the profiler?

Renato

> --
> You received this message because you are subscribed to the Google
> Groups "NGLess" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to ngless+un...@googlegroups.com
> <mailto:ngless+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/ngless/46f31035-f920-4479-ae43-177e380bf230%40googlegroups.com
> <https://groups.google.com/d/msgid/ngless/46f31035-f920-4479-ae43-177e380bf230%40googlegroups.com?utm_medium=email&utm_source=footer>.

--
Renato Alves, PhD
EMBL Bio-IT & HD-HuB (ELIXIR Germany)
EMBL - Meyerhofstr. 1, 69117 Heidelberg, Germany

Lab Phone: +49 6221 387 8150
Email: renato...@embl.de
orcid.org/0000-0002-7212-0234

Github/Gitlab: @unode - Twitter: @renato_alvs

[Luis Pedro Coelho]

Dear List,

Just FYI: we do have some internal versions of these resources that we are trying to package up for public consumption. You can reach out to test them, but we will release them soon for everyone.

Unfortunately, these types of things are much harder to develop than the code as just testing them can easily take a few hours of compute.

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885

> an email to ngless+un...@googlegroups.com.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/ngless/423e6854-5081-15ed-e777-8acb4985f7f6%40embl.de.
>
> Attachments:
> * signature.asc