Comments (6)
Dear Luca,
I've made some very minor changes to your dockerfile.
- I commented out lines 44 and 45 which tries to download and verify gpg keys, cause that killed the docker build command for me.
- I added a line after line 60: ENV PATH $PATH:/galig/asgal
just to have asgal show up without the full path, but as just another command in this environment.
And otherwise, your Dockerfile is pretty much PERFECT. I tested it out and I have zero complains.
Thank you for all your support, Luca.
You have been incredibly helpful and supportive throughout this entire process. I really respect that.
Cheers,
Amit
from galig.
Dear @amitfenn
Let us try to fix this dockerfile once and for all.
I have created a new branch (https://github.com/AlgoLab/galig/tree/issue-%237) with a docker
directory.
Please clone the repo, switch to the issue-#7
branch, go to the docker
dir and issue the follwing commands:
docker build -t algolab/asgal:v1.1.1 .
cd ../example
tar xvzf input.tar.gz
docker run -v $(pwd)/input:/data algolab/asgal:v1.1.1
On my computer, it works™️ ;-)
Thanks for your understanding
from galig.
Hi Again, Luca.
Thanks for maintaining ASGAL. I noticed your dockerfile doesn't build anymore. I get the following error message at line: 38 of your Dockerfile
* CXX /galig/src/utils.cpp
cc1plus: error: bad value ('tigerlake') for '-march=' switch
cc1plus: note: valid arguments to '-march=' switch are: nocona core2 nehalem corei7 westmere sandybridge corei7-avx ivybridge core-avx-i haswell core-avx2 broadwell skylake skylake-avx512 cannonlake icelake-client icelake-server cascadelake bonnell atom silvermont slm goldmont goldmont-plus tremont knl knm x86-64 eden-x2 nano nano-1000 nano-2000 nano-3000 nano-x2 eden-x4 nano-x4 k8 k8-sse3 opteron opteron-sse3 athlon64 athlon64-sse3 athlon-fx amdfam10 barcelona bdver1 bdver2 bdver3 bdver4 znver1 znver2 btver1 btver2 native
cc1plus: error: bad value ('tigerlake') for '-mtune=' switch
cc1plus: note: valid arguments to '-mtune=' switch are: nocona core2 nehalem corei7 westmere sandybridge corei7-avx ivybridge core-avx-i haswell core-avx2 broadwell skylake skylake-avx512 cannonlake icelake-client icelake-server cascadelake bonnell atom silvermont slm goldmont goldmont-plus tremont knl knm intel x86-64 eden-x2 nano nano-1000 nano-2000 nano-3000 nano-x2 eden-x4 nano-x4 k8 k8-sse3 opteron opteron-sse3 athlon64 athlon64-sse3 athlon-fx amdfam10 barcelona bdver1 bdver2 bdver3 bdver4 znver1 znver2 btver1 btver2 generic native
make[1]: *** [/galig/Makefile:150: utils.o] Error 1
make: *** [target.mk:17: /galig/obj] Error 2
The command '/bin/sh -c cd galig ; make' returned a non-zero code: 2
Could you please take a second look at the Dockerfile for me?
Thanking you,
Amit.
from galig.
Dear @amitfenn
Can you confirm that you have tried to build ASGAL on a Tigerlake cpu?
from galig.
Dear Luca,
I was on a Tigerlake cpu. But if this is the problem, please don't spend too much time on this. Asgal Dockerfile works almost perfectly on my server, I just tried it out.
I had to modify "FROM ubuntu:20.04" to "FROM ubuntu:20.10", as some of the apt packages where no longer being shipped for 20.04.
Thanks for your time and your quick response. It is very much appreciated.
Amit.
from galig.
I suspect that the gcc version shipped with ubuntu 20.04 does not support the newest CPUs.
The docker image (i.e. the one you get with a docker pull
) should work on Tigerlake too.
I am leaving this open as a reminder to update the base image to 22.04 once it has been released.
Take care
from galig.
Related Issues (16)
- Asgal (from run in your provided docker): doesn't find Transcript file, looks for gtf instead. HOT 1
- Docker permissions issue HOT 15
- .mem and sam files generated as empty HOT 45
- logs files HOT 2
- Salmon installation not found after pip installation in Asgal HOT 3
- Another permissions question HOT 6
- Adds tmp directory to asgal script
- Novel intron retention events in genome-wide mode HOT 2
- ALK ATI event HOT 9
- Error: Reference genome not found Halting... HOT 1
- Computation of PSI (percent spliced in) HOT 1
- Installation Error: ModuleNotFoundError: No module named 'Bio' HOT 7
- Need help to run the tool, no result for sample.mem HOT 13
- FAILED dependencies of target libtbb; tbb-2018_U3.tgz HOT 15
- Error when testing with example files HOT 3
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 galig.