nextflow installation issue

[Leif Gong]

Dear Nextflow,

I installed Nextflow on linux using the following command and tested fine:

wget -qO- https://get.nextflow.io | bash

after that I had to switch to a different user and run nextflow without internet.  I got the following error:

Downloading nextflow dependencies. It may require a few seconds, please wait .. curl: (6) Could not resolve host: www.nextflow.io; Unknown error

ERROR: Cannot download nextflow required file -- make sure you can connect to the internet

 

Alternatively you can try to download this file:

    https://www.nextflow.io/releases/v0.31.1/nextflow-0.31.1-one.jar

 

and save it as:

    /<home>/.nextflow/framework/0.31.1/nextflow-0.31.1-one.jar

I copied the jar file according to the instruction. Then I got the following error when I run it:

...

CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-api:pom:0.7                                                                          

CAPSULE: Transfer failed: capsule.org.eclipse.aether.transfer.ArtifactTransferException:

…

CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false (for stack trace, run with -Dcapsule.log=verbose)

Unable to initialize nextflow environment

looks like it still needs internet.

Would you please help?

Best,

Leif

[Paolo Di Tommaso]

Nextflow dependencies are installed in the program home that by default is `$HOME/.nextflow`. 

If you need to work offline, you can use the *-all package available for download from GitHub 

https://github.com/nextflow-io/nextflow/releases

p

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[Leif Gong]

sorry, I missed that information. I just tried to run 'sh nextflow-0.31.1-all'. I got an error says "could not download nextflow required file. you can try to download nextflow-0.31.1-all.jar". I couldn't download nextflow-0.31.1-all.jar. I tried again on my own laptop, got the same error below:

$ wget -c https://www.nextflow.io/releases/v0.31.1/nextflow-0.31.1-all.jar

--2018-09-21 05:28:59--  https://www.nextflow.io/releases/v0.31.1/nextflow-0.31.1-all.jar

Resolving www.nextflow.io (www.nextflow.io)... 52.84.33.114, 52.84.33.40, 52.84.33.190, ...

Connecting to www.nextflow.io (www.nextflow.io)|52.84.33.114|:443... connected.

HTTP request sent, awaiting response... 403 Forbidden

2018-09-21 05:29:00 ERROR 403: Forbidden.

Best,

Leif

[Paolo Di Tommaso]

You need to use `bash` not `sh`. You can just give execute permission to that file and use as drop-in replacement of the `nextflow` command. 

Cheers,
Paolo

[Leif Gong]

Thank you very much! it is working now.

Best,

Leif