Comments (6)
Have you tried nfcore-chipseq
? (All lower caps). I think this should work. Annoyingly, docker assumes that if it canโt find a repo then it must be private and that itโs an authentication problem. So bit of a misleading error.
Images arenโt pushed to shub currently. Need to fix the docs here.
Phil
from chipseq.
Well I got a different error message for nfcore-chipseq
:
$ singularity pull --name nfcore-chipseq.img docker://nfcore-chipseq
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/library/nfcore-chipseq:latest
ERROR UNAUTHORIZED: authentication required
ERROR Check existence, naming, and permissions
Cleaning up...
ERROR: pulling container failed!
from chipseq.
Sorry, should't reply on my phone! It's a slash, not a hyphen. No hyphens at all, all lower case:
$ singularity pull --name nfcore-chipseq.img docker://nfcore/chipseq
You can tell from the docker pull
command in the box on the right on the image page which has the image path.
Phil
from chipseq.
Hmm, I'm still having the same problem ๐ค
$ singularity pull --name nfcore-chipseq.img docker://nf-core/chipseq
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/nf-core/chipseq:latest
ERROR UNAUTHORIZED: authentication required
ERROR Check existence
from chipseq.
You put a hyphen in again! It's nfcore/chipseq
not nf-core/chipseq
๐ However, I confess that I did not test the command that I wrote above when I wrote it - I just tried it now and I get a similar error.
On closer inspection the reason for this becomes (embarassingly) clear. There are no image builds. So there's nothing to pull.
The last one failed during the R installation step. I remember now that I did see this I think, but we're currently rebuilding the entire container, so I figured that it wasn't worth looking into it any more.
Ok, so in summary:
- Sorry for making you test so many commands! ๐
- We've started making a
nf-core
python helper tool, and I will soon add a subcommand that will automatically handle all of this crap by looking at the pipeline code. So you will never have to go through this again. - We will finish work on the new container soon I hope, at which point the
nfcore/chipseq
container will exist! - For now, running with the
scilifelab/ngi-chipseq
container should be fine. All of the required software is there, though it doesn't reach the level of reproducibility that we're aiming for (but this repo doesn't have a stable release yet, so we'll get there).
Again, apologies for the half-responses over the past few days (I've been travelling around teaching on various courses). Thanks for testing! I'll close this now that we have an explanation I think.
Phil
from chipseq.
Haha, ok good to have it sorted out. My test with scilifelab/ngi-chipseq
container is still running, so it seems to work ok.
from chipseq.
Related Issues (20)
- Provide replicate information explicitly in samplesheet HOT 5
- Header missing is in bowtie2 outputted bam files
- Problem with samplesheet HOT 3
- Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1) HOT 3
- mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9. HOT 18
- Normalisation of bigwig files
- package or namespace load failed for โUpSetRโ HOT 3
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR
- Get rid of checkIfExists for params paths
- minor "samplesheet_pe.csv" format issue
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model!
- Error with NextSeq trimming
- Error running the pipline test in the BWA index step
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3
- There are multiple files for each of the following file names
- Can't run if there is no control
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ 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. ๐๐๐
-
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 โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from chipseq.