Comments (8)
Hi,
I just wanted to let you know that we've resolved this issue by installing version 2.0.1. I'm not totally sure if the wrong sass
binary was in the 2.0.0 release or if it somehow ended up in our pcgr install because of an existing installation, but either way 2.0.1 is now working for us with the example data.
Thanks for your help!
Best,
Mareike
from cpsr.
Dear Mareike,
Thanks for reporting on this. I have a suspicion it could be related to how quarto is able to operate in your HPC environment, see this issue:
I'll have to dig a bit more to understand this, sorry about the inconvenience. Have you tried running with Apptainer/Singularity?
best,
Sigve
from cpsr.
Maybe test quarto check
first and see if that gives you an error?
from cpsr.
Hi Sigve,
Thanks so much for the quick reply!
I've tried the following:
[mcj43@bc11234 ~]$ source /cvmfs/soft.mugqic/root/software/pcgr/pcgr-2.0.0/envs/pcgrr/etc/conda/activate.d/quarto.sh
[mcj43@bc11234 ~]$ quarto check
Quarto 1.4.550
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
ERROR: TypeError: Invalid Version: Dart SDK version: 2.18.2 (stable) (Tue Sep 27 13:24:11 2022 +0200) on "linux_x64"
Stack trace:
at new SemVer (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:27022:19)
at Range.test (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:27432:23)
at satisfies (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:27649:18)
at checkVersion (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98444:14)
at checkVersions (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98470:5)
at eventLoopTick (ext:core/01_core.js:183:11)
at async check (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98424:13)
at async Command.fn (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98710:5)
at async Command.execute (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:8104:13)
at async quarto (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:114999:5)```
from cpsr.
That's so strange. Mareike, is pcgr-2.0.0/envs/pcgrr/bin/sass --version
also giving you 2.18.2
?
This is what the Docker image is giving (I have v1.4.1.9015 locally but should be the same as v2.0.0):
Click
quarto check
Quarto 1.4.550
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.58.3: OK
Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.4.550
Path: /opt/mambaforge/envs/pcgrr/bin
[✓] Checking tools....................OK
TinyTeX: (not installed)
Chromium: (not installed)
[✓] Checking LaTeX....................OK
Tex: (not detected)
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.12.3 (Conda)
Path: /opt/mambaforge/envs/pcgrr/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[✓] Checking R installation...........OK
Version: 4.3.3
Path: /opt/mambaforge/envs/pcgrr/lib/R
LibPaths:
- /opt/mambaforge/envs/pcgrr/lib/R/library
knitr: 1.47
rmarkdown: 2.27
[✓] Checking Knitr engine render......OK
The Dart Sass version is the same as the conda lockfile at https://github.com/sigven/pcgr/blob/main/conda/env/lock/pcgrr-linux-64.lock#L8
from cpsr.
Yes, I'm getting the same version:
[mcj43@bc11234 ~]$ /cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/sass --version
Dart SDK version: 2.18.2 (stable) (Tue Sep 27 13:24:11 2022 +0200) on "linux_x64"
from cpsr.
I'm flying completely blind here but maybe you could try replacing that sass
binary with the one from https://github.com/sass/dart-sass/releases/tag/1.58.3. Under assets I think you'll need the dart-sass-1.58.3-linux-x64.tar.gz
one. Decompress and there should be a sass
binary in the dart-sass
folder. Let's see if that does anything.
from cpsr.
We'll give it a shot! Thanks!
from cpsr.
Related Issues (20)
- Missed variant due to transcript pick? HOT 9
- cpsr_configuration_default.toml missing from PCGR data HOT 2
- Error: Problem with `mutate()` input `ACMG_PVS1_1`. HOT 4
- Error in loadNamespace(name) : there is no package called 'reactable' HOT 2
- x object 'GWAS_CITATION' not found HOT 3
- ImportError: No module named toml HOT 1
- minor typo in src/cpsr_functions.R HOT 1
- Error: `x` and `y` must share the same src HOT 5
- genes being excluded from CPSR exploratory track HOT 5
- Not able to download the data bundles (404 Error) HOT 2
- ACMG guideline updated to version 3.0. New genes were added to the secondary finding gene list. HOT 2
- make infromation like ckb to cpsr HOT 4
- Encounter the error in cpsr-report-generation() HOT 3
- Installation Instructions Only Describe Conda HOT 2
- Add sif file for running on an HPC HOT 1
- Biomarker variants not in Pathogenic/Likely Pathogenic section of report HOT 1
- adding clones IDs + child clone emerging outside parent clone HOT 2
- Feature Request - support CNV calls (and ideally SV calls) HOT 5
- incorrect permissions when copying templates dir with file.copy() HOT 9
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cpsr.