Thanks for the information. I've seen this error before, but only when using an external (and incompatible) nodejs. It looks like, in your case, it's correctly using .venv/bin/node that Galaxy will have installed. Can you check the version of that for me with `
/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node --version`? And is there another node/yarn available on the system?
It might also be useful information to see what happens when you try the client build directly, both within the .venv and without, so, from the Galaxy directory try a `make client`. Save the output of that, and then `source .venv/bin/activate`, and `make client` again.
-Dannon
On Tue, Jan 8, 2019 at 11:15 AM Matthias Bernt <
m.bernt@ufz.de> wrote:
Hi Dannon,
We are trying to run release_18.09.
Indeed the output was from planemo, but we get the same (yarn) error
when ./run.sh is called without planemo:
```
$ NODE_ENV=production gulp staging && concurrently "yarn run style"
"yarn run webpack-production-maps" "yarn run gulp clean && yarn run
gulp-production-maps" && yarn run save-build-hash
gulp[14831]: ../src/node_contextify.cc:628:static void
node::contextify::ContextifyScript::New(const
v8::FunctionCallbackInfo<v8::Value>&): Assertion `args[1]->IsString()'
failed.
1: 0x8daaa0 node::Abort() [gulp]
2: 0x8dab75 [gulp]
3: 0x90e2f7
node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value>
const&) [gulp]
4: 0xb5e71b [gulp]
5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int,
v8::internal::Object**, v8::internal::Isolate*) [gulp]
6: 0x2ce8440dbe1d
/tmp/yarn--1546961268610-0.24122682361732672/node: line 3: 14831
Aborted (core dumped)
"/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node"
"$@"
error Command failed with exit code 134.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about
this command.
ERROR: Galaxy client build failed. See ./client/README.md for more
information, including how to get help.
```
Best,
Matthias
On 08.01.19 16:09, Dannon Baker wrote:
> What version of Galaxy exactly is this? And, it looks like it's being
> run by planemo, and not a simple 'run.sh' via the command line -- is
> that correct?
>
> On Tue, Jan 8, 2019 at 10:04 AM Matthias Bernt <m.bernt@ufz.de
> <mailto:m.bernt@ufz.de>> wrote:
>
> Dear all,
>
> a colleague tries to run.sh on a Manjaro Linux and got the following
> error:
>
>
> ```
> yarn run v1.12.3
> $ NODE_ENV=production gulp staging && concurrently "yarn run style"
> "yarn run webpack-production-maps" "yarn run gulp clean && yarn run
> gulp-production-maps" && yarn run save-build-hash
> gulp[12888]: ../src/node_contextify.cc:628:static void
> node::contextify::ContextifyScript::New(const
> v8::FunctionCallbackInfo<v8::Value>&): Assertion `args[1]->IsString()'
> failed.
> 1: 0x8daaa0 node::Abort() [gulp]
> 2: 0x8dab75 [gulp]
> 3: 0x90e2f7
> node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value>
> const&) [gulp]
> 4: 0xb5e71b [gulp]
> 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int,
> v8::internal::Object**, v8::internal::Isolate*) [gulp]
> 6: 0x6f20bcdbe1d
> /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888
> Aborted (core dumped)
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node"
> "$@"
> error Command failed with exit code 134.
> info Visit https://yarnpkg.com/en/docs/cli/run for documentation about
> this command.
> ERROR: Galaxy client build failed. See ./client/README.md for more
> information, including how to get help.
> Problem running Galaxy command [].
> Traceback (most recent call last):
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo",
> line 11, in <module>
> sys.exit(planemo())
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 764, in __call__
> return self.main(*args, **kwargs)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 717, in main
> rv = self.invoke(ctx)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 1137, in invoke
> return _process_result(sub_ctx.command.invoke(sub_ctx))
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 956, in invoke
> return ctx.invoke(self.callback, **ctx.params)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 555, in invoke
> return callback(*args, **kwargs)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py",
> line 64, in new_func
> return ctx.invoke(f, obj, *args, **kwargs)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 555, in invoke
> return callback(*args, **kwargs)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py",
> line 195, in handle_blended_options
> return f(*args, **kwds)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py",
> line 43, in cli
> galaxy_serve(ctx, runnables, **kwds)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py",
> line 22, in serve
> return _serve(ctx, runnables, **kwds)
> File
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py",
> line 54, in _serve
> raise Exception(message)
> Exception: Problem running Galaxy command [].
> ```
>
> Would be great to have a suggestion...
>
> Cheers,
> Matthias
>
>
> --
>
> -------------------------------------------
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> -------------------------------------------
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
-------------------------------------------