search

MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
13 stars 5 forks source link

Installation Instructions Unclear #15

Closed andrewyatz closed 6 years ago

andrewyatz commented 6 years ago

Hi there

I am reviewing your JOSS paper submission. I have been trying to run your Ansible playbooks as detailed here https://monashbioinformaticsplatform.github.io/RNAsik-pipe/docs/#installation however the procedure does not work. Running this on my Mac I get the following response:

$ ansible-playbook -i host bio.yml --tags bds,rnasik,star,bwa,hisat2,subread,samtools,htslib,bedtools,picard,qualimap,fastqc,multiqc
 [WARNING]: Unable to parse /Users/ayates/rnasik/bio-ansible/host as an inventory source

 [WARNING]: No inventory was parsed, only implicit localhost is available

 [WARNING]: provided hosts list is empty, only localhost is available. Note that the implicit localhost does not match 'all'

[DEPRECATION WARNING]: The use of 'include' for tasks has been deprecated. Use 'import_tasks' for static inclusions or 'include_tasks' for dynamic inclusions. This feature will
be removed in a future release. Deprecation warnings can be disabled by setting deprecation_warnings=False in ansible.cfg.
[DEPRECATION WARNING]: include is kept for backwards compatibility but usage is discouraged. The module documentation details page may explain more about this rationale.. This
feature will be removed in a future release. Deprecation warnings can be disabled by setting deprecation_warnings=False in ansible.cfg.
[DEPRECATION WARNING]: Specifying include variables at the top-level of the task is deprecated. Please see: http://docs.ansible.com/ansible/playbooks_roles.html#task-include-
files-and-encouraging-reuse   for currently supported syntax regarding included files and variables. This feature will be removed in version 2.7. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
 [WARNING]: Could not match supplied host pattern, ignoring: bio

PLAY [Installing bioinformatics tools] *******************************************************************************************************************************************
skipping: no hosts matched

PLAY RECAP ***********************************************************************************************************************************************************************

I am running Ansible v2.4.3.0 and updated to this version this morning. Can you please look into this or alter your installation documentation to clarify the requirements to run your playbook.

Thanks

serine commented 6 years ago

@andrewyatz sorry about that, it was a typo in the docs, fixed now. It was meant to be hosts not host file. You should find that file inside bio-ansible repository. It is an inventory file that you can specify different remote machines (servers). Idea of ansible is that you could install RNAsik (or any other of bio-ansible tasks) on multiple machines with one command given that you've put those machine's IP address into inventory file. For a purpose of single installation local (localhost) i.e your current machine is all you need, which is default inside hosts file

Give another go now that the docs have been updated

Thanks