Comments (15)
gdv
commented on July 29, 2024
May you please include some information on your system (e.g. which operating system/distribution), and on the contents of the input dir?
from galig.
husamia
commented on July 29, 2024
May you please include some information on your system (e.g. which operating system/distribution), and on the contents of the
inputdir?
I am using Docker Desktop on Windows and input is the sample data
from galig.
gdv
commented on July 29, 2024
Did you also run
wget https://github.com/AlgoLab/galig/raw/master/example/input.tar.gz
tar xfz input.tar.gz
before running asgal? The error message you got usually happens when the input directory has not been created before.
from galig.
husamia
commented on July 29, 2024
yes, I did that.
…On Sun, Nov 15, 2020 at 11:53 AM Gianluca Della Vedova < ***@***.***> wrote:
Did you also run
wget https://github.com/AlgoLab/galig/raw/master/example/input.tar.gz
tar xfz input.tar.gz
before running asgal? The error message you got usually happens when the
input directory has not been created before.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#11 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ADGRHUFPEM3X2TX6MQK3VU3SQABRVANCNFSM4TUVJEPA>
.
from galig.
gdv
commented on July 29, 2024
May I ask you to provide the contents (and permissions) of the current directory and of the input directory?
Sorry, but I don't have a Windows machine to try to replicate your situation.
Take care
from galig.
husamia
commented on July 29, 2024
drwxrwxrwx 1 root root 4.0K Nov 25 2019 input
…-rwxrwxrwx 1 root root 15K Jan 28 2018 annotation.gtf
-rwxrwxrwx 1 root root 23M Jan 28 2018 genome.fa
-rwxrwxrwx 1 root root 3.2M Jan 28 2018 sample_1.fa
It's not Windows problem. I am using WSL
On Mon, Nov 16, 2020 at 2:14 AM Gianluca Della Vedova < ***@***.***> wrote:
May I ask you to provide the contents (and permissions) of the current
directory and of the input directory?
Sorry, but I don't have a Windows machine to try to replicate your
situation.
Take care
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#11 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ADGRHUAPAAUUTUGWID2DO53SQDGOVANCNFSM4TUVJEPA>
.
from galig.
gdv
commented on July 29, 2024
Ok, then the problem is some sort of interaction with WSL. We expect that the input directory is owned by a regular user, not root.
I am going to update the docker image shortly to take into account this issue.
Thanks for the report.
from galig.
husamia
commented on July 29, 2024
Do you know how to pull the latest docker container with the fix?
from galig.
gdv
commented on July 29, 2024
If you delete the image with `docker rmi`, the next `docker run` should
pull the updated container.
You can use `docker images` to see the list of your images.
Take care
Gianluca Della Vedova
https://gianluca.dellavedova.org
…On 17/11/2020 at 17:37, husamia wrote:
Do you know how to pull the latest docker container with the fix?
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub, or unsubscribe.*
from galig.
husamia
commented on July 29, 2024
When I try to delete I get an error that another container is using it but I don't have that container
docker rmi d9fa1ddd9d21
Error response from daemon: conflict: unable to delete d9fa1ddd9d21 (must be forced) - image is being used by stopped container 4d03f790f96d
so I force delete it and when I pull it, it seems to not pulling the latest update for some reason..
from galig.
gdv
commented on July 29, 2024
I have uploaded a new image to docker hub.
May you please try docker run -v "$PWD"/input:/data algolab/asgal:v1.1.2 ?
from galig.
husamia
commented on July 29, 2024
It's working now. I can't pass arguments using interactive mode i.e. -it with docker and bash.
from galig.
gdv
commented on July 29, 2024
The docker image has not been designed for interactive use.
What do you want to achieve? Maybe there is another way.
from galig.
husamia
commented on July 29, 2024
I want to do genome-wide analysis with my own data from RNA-Seq using docker container. I want to create new annotations from ensembl for GRCh38.
from galig.
gdv
commented on July 29, 2024
In this case, you should just copy your files into the input directory
(or use a different directory in the `-v` option of `docker run`).
The filenames must be the same as those used in the sample dataset.
If you want to use different filenames, you need to compile asgal
instead of using the docker image.
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
- .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
- Issues with Dockerfile HOT 6
- 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.