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Support #30

Support #24: Setting up the NGI-RNAseq pipeline on UCT Hex

Support #25: Configure NGI-RNAseq pipeline to run on hex

Update Nextflow to version 0.27.6

Added by Katie Lennard about 7 years ago. Updated about 7 years ago.

Status:
In Progress
Priority:
Normal
Assignee:
Gerrit Botha
Start date:
04/09/2018
Due date:
% Done:

0%

Estimated time:

Description

The RNAseq pipeline requires an updated version of Nextflow (currently 0.26.3, need 0.27.6)

History

#1

Updated by Gerrit Botha about 7 years ago

  • Status changed from New to In Progress

Ok Katie, will do it in the next hour or so. Will get back to you.

#2

Updated by Gerrit Botha about 7 years ago

Ok it is setup in /opt/exp_soft/cbio/nextflow

Add the following lines in your .bashrc

JAVA_CMD=/opt/exp_soft/java/jdk1.8.0_31/bin/java
JAVA_HOME=/opt/exp_soft/java/jdk1.8.0_31/
export PATH=$PATH:/opt/exp_soft/cbio/nextflow


/opt/exp_soft/cbio/nextflow/nextflow -v
nextflow version 0.28.0.4779

So it is version 0.28.0.4779 do you need exactly 0.27.6 though?

#3

Updated by Katie Lennard about 7 years ago

Gerrit Botha wrote:

Ok it is setup in /opt/exp_soft/cbio/nextflow

Add the following lines in your .bashrc

JAVA_CMD=/opt/exp_soft/java/jdk1.8.0_31/bin/java
JAVA_HOME=/opt/exp_soft/java/jdk1.8.0_31/
export PATH=$PATH:/opt/exp_soft/cbio/nextflow


/opt/exp_soft/cbio/nextflow/nextflow -v
nextflow version 0.28.0.4779

So it is version 0.28.0.4779 do you need exactly 0.27.6 though?

Thanks Gerrit, I'm not sure. The error message says "Nextflow version 0.27.6 required" Will test and let you know..

#4

Updated by Katie Lennard about 7 years ago

Have added lines to .bashrc but can't test nextflow (version -v):

/bin/bash: /opt/exp_soft/cbio/nextflow/nextflow: Permission denied

#5

Updated by Gerrit Botha about 7 years ago

Try again. I opened up read permissions to the binary.

#6

Updated by Katie Lennard about 7 years ago

Gerrit Botha wrote:

Try again. I opened up read permissions to the binary.

Hmmm, kry nou:
Downloading nextflow dependencies. It may require a few seconds, please wait .. curl: (59) failed setting cipher list
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/v0.28.0/nextflow-0.28.0-one.jar

and save it as:
/home/kviljoen/.nextflow/framework/0.28.0/nextflow-0.28.0-one.jar

Het bashrc verander so nie seker watse depencies vermis word nie.

#7

Updated by Katie Lennard about 7 years ago

Katie Lennard wrote:

Gerrit Botha wrote:

Try again. I opened up read permissions to the binary.

Hmmm, kry nou:
Downloading nextflow dependencies. It may require a few seconds, please wait .. curl: (59) failed setting cipher list
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/v0.28.0/nextflow-0.28.0-one.jar

and save it as:
/home/kviljoen/.nextflow/framework/0.28.0/nextflow-0.28.0-one.jar

Het bashrc verander so nie seker watse depencies vermis word nie.

Lyk my dis 'n workernode-specific issue. As ek /opt/exp_soft/cbio/nextflow/nextflow -v van die headnode hardloop:
CAPSULE: Downloading dependency org.jsoup:jsoup:pom:1.11.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:pom:2.4.13
CAPSULE: Downloading dependency io.nextflow:nxf-s3fs:pom:1.0.3
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:pom:2.4.13
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:pom:2.4.13
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:pom:2.4.13
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:pom:2.4.13
CAPSULE: Downloading dependency io.nextflow:nextflow:pom:0.28.0
CAPSULE: Downloading dependency io.nextflow:nxf-commons:pom:0.28.0
CAPSULE: Downloading dependency io.nextflow:nxf-httpfs:pom:0.28.0
CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.11.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:2.4.13
CAPSULE: Downloading dependency io.nextflow:nxf-s3fs:jar:1.0.3
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:2.4.13
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:2.4.13
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:2.4.13
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:2.4.13
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:0.28.0
CAPSULE: Downloading dependency io.nextflow:nxf-commons:jar:0.28.0
CAPSULE: Downloading dependency io.nextflow:nxf-httpfs:jar:0.28.0
nextflow version 0.28.0.4779

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