Cannot install and following the instructions

[andrewyatz]

Have to reopen this I'm sorry. So I've just tried to run this on vagrant/virtualbox using Ubuntu 16.04 as suggested. Firstly I think your docs should be updated to first issue a sudo apt-get update ensuring apt is ready to install. Secondly you should add --yes to your install commands as it will make it a lot easier to copy and paste the commands to run them. That's the good news.

Bad news. I got to running bioansible as prescribed on the ubuntu VM and get the following output

$ ansible-playbook -i hosts bio.yml --tags dirs,bds,rnasik,star,bwa,hisat2,subread,samtools,htslib,bedtools,picard,qualimap,fastqc,multiqc
[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.

PLAY [Installing bioinformatics tools] ******************************************************************************************************************************************************************************************************

TASK [Gathering Facts] **********************************************************************************************************************************************************************************************************************
ok: [localhost]

TASK [make_dirs : Create required directories] **********************************************************************************************************************************************************************************************
failed: [localhost] (item=/home/vagrant/bioansible/software/source) => {"changed": false, "gid": 1000, "group": "vagrant", "item": "/home/vagrant/bioansible/software/source", "mode": "0775", "msg": "chown failed: failed to look up user ubuntu", "owner": "vagrant", "path": "/home/vagrant/bioansible", "size": 4096, "state": "directory", "uid": 1000}
failed: [localhost] (item=/home/vagrant/bioansible/software/modules) => {"changed": false, "gid": 1000, "group": "vagrant", "item": "/home/vagrant/bioansible/software/modules", "mode": "0775", "msg": "chown failed: failed to look up user ubuntu", "owner": "vagrant", "path": "/home/vagrant/bioansible/software", "size": 4096, "state": "directory", "uid": 1000}
failed: [localhost] (item=/home/vagrant/bioansible/software/modules/core) => {"changed": false, "gid": 1000, "group": "vagrant", "item": "/home/vagrant/bioansible/software/modules/core", "mode": "0775", "msg": "chown failed: failed to look up user ubuntu", "owner": "vagrant", "path": "/home/vagrant/bioansible/software/modules", "size": 4096, "state": "directory", "uid": 1000}
failed: [localhost] (item=/home/vagrant/bioansible/software/modules/bio) => {"changed": false, "gid": 1000, "group": "vagrant", "item": "/home/vagrant/bioansible/software/modules/bio", "mode": "0775", "msg": "chown failed: failed to look up user ubuntu", "owner": "vagrant", "path": "/home/vagrant/bioansible/software/modules/bio", "size": 4096, "state": "directory", "uid": 1000}
failed: [localhost] (item=/home/vagrant/bioansible/software/modules/extra) => {"changed": false, "gid": 1000, "group": "vagrant", "item": "/home/vagrant/bioansible/software/modules/extra", "mode": "0775", "msg": "chown failed: failed to look up user ubuntu", "owner": "vagrant", "path": "/home/vagrant/bioansible/software/modules/extra", "size": 4096, "state": "directory", "uid": 1000}
failed: [localhost] (item=/home/vagrant/bioansible/software/apps) => {"changed": false, "gid": 1000, "group": "vagrant", "item": "/home/vagrant/bioansible/software/apps", "mode": "0775", "msg": "chown failed: failed to look up user ubuntu", "owner": "vagrant", "path": "/home/vagrant/bioansible/software/apps", "size": 4096, "state": "directory", "uid": 1000}
    to retry, use: --limit @/home/vagrant/bio-ansible/bio.retry

PLAY RECAP **********************************************************************************************************************************************************************************************************************************
localhost                  : ok=1    changed=0    unreachable=0    failed=1]

Honestly I don't know what is wrong here. There must be an issue in how these directories are being created but I don't know what that is. Please can you take a look.

[serine]

@andrewyatz, looks like your username on that VM is vagrant. could you set that in group_vars/all under main_guy: vagrant? This should solve your problem.

This is a bit annoying it should auto detect localhost username, but for some reason I'm struggling to do that through ansible, hopefully will be able to fix in the future

[serine]

@andrewyatz going to close this issue for now, feel free to reopen it again if you need to. As I've mentioned on the other channel, you can now simply install with conda install more info here