artbio / galaxykickstart Goto Github PK

I would propose to use travis CI. It appears we could both test test the playbook, and testing the underlying galaxy installation. @bgruening has done an awesome job for docker-galaxy-stable (https://github.com/bgruening/docker-galaxy-stable/blob/dev/.travis.yml).

So let's

• test succesfull playbook execution
• test building docker-artimed images
• test that galaxy can do some basic things (FTP up, run workflows ...)
• test managing/migrating a running instance
• migrate travis testing into a role/playbook section
• put travis.yml testing scripts into bash/tox scripts
• use travis to test code snippets from the documentation
• long tool installtions time-out with travis -> setup jenkins on IFB cloud

Showstoppers:

• installation of tools takes a very long time - > trim down the amount of datamanagers. Perhaps only fasta and bowtie2/bwa ?

in the running instance, the prompt for user says something not appropriate: a name which is not a full name and a port 2121.

Should be as simple as handling these variables:

galaxy_extras_config_ie_proxy: true

galaxy_extras_ie_fetch_ipython: false
galaxy_extras_ie_ipython_image: bgruening/docker-ipython-notebook:dev
galaxy_extras_ie_fetch_rstudio: false
galaxy_extras_ie_rstudio_image: erasche/docker-rstudio-notebook:dev

galaxy_docker_enabled: false
galaxy_docker_sudo: false
galaxy_docker_volumes_from: galaxy
galaxy_docker_volumes : "$defaults"

in https://github.com/ARTbio/ansible-artimed/blob/master/galaxy/install.sh#L87
in seems that $USER will be empty by default, is it a bug or a feature ?

Since the clinicians are probably only working with human data.

And deposit workflow in a repository.

I tested the galaxy-ansible server install on the IFB cloud and it seems to work.
In contrast, the current command line stated in the readme file
https://github.com/ARTbio/ansible-artimed/blob/master/README.md#installing-galaxy-ngs-tools
does not work.

We could get it working by symlinking ln -s ../../roles/ from the artimed_extras directory. But it's a hack.
The idea, if I catch properly, is not mixing playbooks and roles, ie, not having a playbook in a role folder and vice versa

version d20e36a

seems a bit odd

https://github.com/galaxyproject/ansible-galaxy-os

This is necessary for interacting with the api to install tools or workflows.

in https://github.com/ARTbio/ansible-artimed/blob/master/README.md, why the sh script is run in the third line, whereas it is apparently required at the very beginning to install pip, git et bla bla...
I'll test anyway...

We need a documentation that explains how to generate or adapt this file for specific purpose
https://github.com/ARTbio/ansible-artimed/blob/master/roles/artimed_extras/files/artimed_tool_list.yaml

the init.d galaxy service is not loaded automatically at restart of the machin (in amazon instance at least).
Please review this step of the deployment

Started to follow the recipe in https://github.com/ARTbio/ansible-artimed/blob/master/README.md

First, I add to install apt-get install git. Thus this recipe is missing something there.
Second, I did this, and I got an error due to an already existing cd.

git clone --recursive https://github.com/ARTbio/ansible-artimed.git
Cloning into 'ansible-artimed'...
Username for 'https://github.com': drosofff
Password for 'https://[email protected]':
remote: Counting objects: 1030, done.
remote: Total 1030 (delta 0), reused 0 (delta 0), pack-reused 1030
Receiving objects: 100% (1030/1030), 1.49 MiB | 0 bytes/s, done.
Resolving deltas: 100% (499/499), done.
Checking connectivity... done.
Submodule 'galaxy_vm/roles/galaxyprojectdotorg.galaxy' (git://github.com/galaxyproject/ansible-galaxy) registered for path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy'
Submodule 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-extras' (git://github.com/galaxyproject/ansible-galaxy-extras) registered for path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-extras'
Submodule 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-os' (git://github.com/galaxyproject/ansible-galaxy-os) registered for path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-os'
Submodule 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-tools' (git://github.com/galaxyproject/ansible-galaxy-tools) registered for path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-tools'
Submodule 'galaxy_vm/roles/natefoo.postgresql_objects' (git://github.com/natefoo/ansible-postgresql-objects) registered for path 'galaxy_vm/roles/natefoo.postgresql_objects'
Cloning into 'galaxy_vm/roles/galaxyprojectdotorg.galaxy'...
remote: Counting objects: 147, done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 147 (delta 3), reused 0 (delta 0), pack-reused 137
Receiving objects: 100% (147/147), 27.70 KiB | 0 bytes/s, done.
Resolving deltas: 100% (67/67), done.
Checking connectivity... done.
Submodule path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy': checked out 'b8886463194ed66c22c2a810956b84b2ed551638'
Cloning into 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-extras'...
remote: Counting objects: 355, done.
remote: Total 355 (delta 0), reused 0 (delta 0), pack-reused 355
Receiving objects: 100% (355/355), 55.90 KiB | 0 bytes/s, done.
Resolving deltas: 100% (219/219), done.
Checking connectivity... done.
Submodule path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-extras': checked out 'f0cdf3b3a53875a8498dc478781c112c5de2c4b2'
Cloning into 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-os'...
remote: Counting objects: 72, done.
remote: Total 72 (delta 0), reused 0 (delta 0), pack-reused 72
Receiving objects: 100% (72/72), 11.73 KiB | 0 bytes/s, done.
Resolving deltas: 100% (28/28), done.
Checking connectivity... done.
Submodule path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-os': checked out '58c3b61ab37672146a46d95f0671337f39b13a31'
Cloning into 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-tools'...
remote: Counting objects: 148, done.
remote: Total 148 (delta 0), reused 0 (delta 0), pack-reused 148
Receiving objects: 100% (148/148), 37.91 KiB | 0 bytes/s, done.
Resolving deltas: 100% (69/69), done.
Checking connectivity... done.
Submodule path 'galaxy_vm/roles/galaxyprojectdotorg.galaxy-tools': checked out '0f175fda7bc85d5fec136a6bb9102bee0f2326b8'
Cloning into 'galaxy_vm/roles/natefoo.postgresql_objects'...
remote: Counting objects: 22, done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 22 (delta 5), reused 22 (delta 5), pack-reused 0
Receiving objects: 100% (22/22), 6.75 KiB | 0 bytes/s, done.
Resolving deltas: 100% (5/5), done.
Checking connectivity... done.
Submodule path 'galaxy_vm/roles/natefoo.postgresql_objects': checked out '81179c442016a1d5856d18252d89103a3da15be3'
ubuntu@ip-172-30-0-137:$ cd ansible-artimed/galaxy_vm
ubuntu@ip-172-30-0-137:/ansible-artimed/galaxy_vm$ bash install.sh
sudo: unable to resolve host ip-172-30-0-137
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package virtualbox is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'virtualbox' has no installation candidate
sudo: unable to resolve host ip-172-30-0-137
gpg: keyring /tmp/tmpnu_ajvyr/secring.gpg' created gpg: keyring/tmp/tmpnu_ajvyr/pubring.gpg' created
gpg: requesting key 7BB9C367 from hkp server keyserver.ubuntu.com
gpg: /tmp/tmpnu_ajvyr/trustdb.gpg: trustdb created
gpg: key 7BB9C367: public key "Launchpad PPA for Ansible, Inc." imported
gpg: Total number processed: 1
gpg: imported: 1 (RSA: 1)
OK
sudo: unable to resolve host ip-172-30-0-137
Ign http://us-east-1.ec2.archive.ubuntu.com trusty InRelease
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Fetched 10.3 MB in 2s (4,122 kB/s)
Reading package lists... Done
sudo: unable to resolve host ip-172-30-0-137
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
binutils build-essential cpp cpp-4.8 dpkg-dev fakeroot g++ g++-4.8 gcc
gcc-4.8 gcc-4.8-base libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libasan0 libatomic1 libc-dev-bin libc6-dev
libcloog-isl4 libdpkg-perl libfakeroot libfile-fcntllock-perl libgcc-4.8-dev
libgmp10 libgomp1 libisl10 libitm1 libmpc3 libmpfr4 libpython2.7
libpython2.7-minimal libpython2.7-stdlib libquadmath0 libstdc++-4.8-dev
libstdc++6 libtsan0 linux-libc-dev make manpages-dev python-chardet-whl
python-colorama python-colorama-whl python-crypto python-distlib
python-distlib-whl python-html5lib python-html5lib-whl python-httplib2
python-jinja2 python-markupsafe python-paramiko python-pip-whl
python-pkg-resources python-requests-whl python-setuptools
python-setuptools-whl python-six-whl python-support python-urllib3-whl
python-wheel python2.7-minimal python3-pkg-resources
python3-software-properties sshpass
Suggested packages:
binutils-doc cpp-doc gcc-4.8-locales debian-keyring g++-multilib
g++-4.8-multilib gcc-4.8-doc libstdc++6-4.8-dbg gcc-multilib autoconf
automake1.9 libtool flex bison gdb gcc-doc gcc-4.8-multilib libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan0-dbg libtsan0-dbg
libquadmath0-dbg glibc-doc libstdc++-4.8-doc make-doc python-crypto-dbg
python-crypto-doc python-genshi python-lxml python-jinja2-doc
python-distribute python-distribute-doc python2.7-doc binfmt-support
python3-setuptools
Recommended packages:
python-dev-all
The following NEW packages will be installed:
ansible binutils build-essential cpp cpp-4.8 dpkg-dev fakeroot g++ g++-4.8
gcc gcc-4.8 libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libasan0 libatomic1 libc-dev-bin libc6-dev
libcloog-isl4 libdpkg-perl libfakeroot libfile-fcntllock-perl libgcc-4.8-dev
libgmp10 libgomp1 libisl10 libitm1 libmpc3 libmpfr4 libquadmath0
libstdc++-4.8-dev libtsan0 linux-libc-dev make manpages-dev
python-chardet-whl python-colorama python-colorama-whl python-crypto
python-distlib python-distlib-whl python-html5lib python-html5lib-whl
python-httplib2 python-jinja2 python-markupsafe python-paramiko python-pip
python-pip-whl python-requests-whl python-setuptools python-setuptools-whl
python-six-whl python-support python-urllib3-whl python-virtualenv
python-wheel python3-pkg-resources sshpass
The following packages will be upgraded:
gcc-4.8-base libpython2.7 libpython2.7-minimal libpython2.7-stdlib
libstdc++6 python-pkg-resources python2.7 python2.7-minimal
python3-software-properties software-properties-common
10 upgraded, 59 newly installed, 0 to remove and 115 not upgraded.
Need to get 45.9 MB of archives.
After this operation, 126 MB of additional disk space will be used.
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fatal: destination path '/home/ubuntu/ansible-artimed' already exists and is not an empty directory.

@fabiorjvieira The playbook must respect the ansible logics: only one ansible-playbook command with the option to add or not tools. Right now, having to navigate in the cloned repo and type another ansible-playbook command is unclear and error-prone for the end user.

does not enable FTP over TLS. Does that mean that the playbook configure proftpd for working over TLS, which is not supported by Amazon ?

Statut :            Connexion à 52.90.58.200:21...
Statut :            Connexion établie, attente du message d'accueil...
Statut :            Serveur non sécurisé, celui-ci ne supporte pas FTP sur TLS.
Commande :  USER [email protected]
Réponse :      331 Password required for [email protected]
Commande :  PASS ***********
Erreur :            Connexion interrompue par le serveur
Erreur :            Impossible d'établir une connexion au serveur
Statut :            Attente avant nouvel essai...
Statut :            Connexion à 52.90.58.200:21...
Statut :            Connexion établie, attente du message d'accueil...
Réponse :      220 ProFTPD 1.3.5rc3 Server (Galaxy ARTiMED FTP server!) [::ffff:172.30.1.160]
Commande :  AUTH TLS
Réponse :      500 AUTH not understood
Commande :  AUTH SSL
Réponse :      500 AUTH not understood
Statut :            Serveur non sécurisé, celui-ci ne supporte pas FTP sur TLS.

@fabiorjvieira
I see you're heavily modifying the dev branch, which is good obviously.
But I think you could really profit from using a branch per feature or bug.
This would avoid ending up with a huge incompatible merge, like it is now.

Also, this would make it much easier for @drosofff and me to evaluate and comment on the things you do.
Plus you can do regular updates to the master branch, so we can work with it.
For example the changes you are working on for persisting postgresql seem very complex considering a bind-mount should suffice (I could be wrong, but discussing about this in isolation is much easier). Also consider that this is a very standard job, so tested & proven best-practice solutions are likely out there.

In summary, everyone wins if you work with one branch per feature (and maybe create an issue before working on a feature?).
Looking forward to test your changes ;).

@fabiorjvieira
The issue #20 is associated (not saying this is the cause) to an ansible version in the docker container
root@8b23feb9619a:~# ansible --version
ansible 1.5.4

Here, could you detail how your script, which states "Minimum requirements: OpenSSH client, Ansible >=1.8 and git.", ensures indeed that Ansible is >=1.8 ?

using this version d20e36a

TASK: [artimed_extras | Restart/start supervisor tasks] *********************** 
failed: [52.23.179.74] => (item={'state': 'restarted', 'name': 'proftpd'}) => {"failed": true, "item": {"name": "proftpd", "state": "restarted"}}
msg: proftpd: ERROR (not running)
proftpd: ERROR (abnormal termination)

ok: [52.23.179.74] => (item={'state': 'started', 'name': 'munge'})
ok: [52.23.179.74] => (item={'state': 'started', 'name': 'nginx'})

FATAL: all hosts have already failed -- aborting

PLAY RECAP ******************************************************************** 
           to retry, use: --limit @/Users/chris/galaxy.retry

52.23.179.74               : ok=78   changed=57   unreachable=0    failed=1

and

(.venv-ansible)lbcd-17:ansible-artimed chris$ git diff
diff --git a/hosts b/hosts
index 5b0152c..479924d 100644
--- a/hosts
+++ b/hosts
@@ -1,17 +1,17 @@
 [artimed]
-localhost ansible_ssh_user="root" ansible_ssh_private_key_file="~/.ssh/id_rsa"
+52.23.179.74 ansible_ssh_user="ubuntu" ansible_ssh_private_key_file="~/.ssh/chriskey1.pem"

 [artimed:vars]
 #install options
 install_galaxy="True"
-install_tools="True"
-run_data_manager="True"
+install_tools="False"
+run_data_manager="False"
 #params
 supervisor_postgres_database_path="/etc/postgresql/{{ postgresql_version }}/main"
 galaxy_user_name="galaxy"
 galaxy_server_dir="/home/{{ galaxy_user_name }}/{{ galaxy_user_name }}"
-galaxy_admin="[email protected]"
-galaxy_admin_pw="artimed"
+galaxy_admin="[email protected]"
+galaxy_admin_pw="metavisitor"
 master_api_key=f137d9af2f2065bd8c5fbadf7111494b
 galaxy_tool_list="roles/artimed_extras/files/artimed_tool_list.yaml"
 galaxy_data_managers="data_managers.yaml"

and the log of proftpd:

root@ip-172-30-0-62:~# tail -f /var/log/supervisor/proftpd-std*
==> /var/log/supervisor/proftpd-stderr---supervisor-jLn7WL.log <==
2016-01-06 16:03:59,857 ip-172-30-0-62 proftpd[8153]: Fatal: error processing configuration file '/etc/proftpd/proftpd.conf'
2016-01-06 16:04:01,665 ip-172-30-0-62 proftpd[8159]: warning: unable to determine IP address of 'ip-172-30-0-62'
2016-01-06 16:04:01,665 ip-172-30-0-62 proftpd[8159]: error: no valid servers configured
2016-01-06 16:04:01,665 ip-172-30-0-62 proftpd[8159]: Fatal: error processing configuration file '/etc/proftpd/proftpd.conf'
2016-01-06 16:04:04,683 ip-172-30-0-62 proftpd[8197]: warning: unable to determine IP address of 'ip-172-30-0-62'
2016-01-06 16:04:04,683 ip-172-30-0-62 proftpd[8197]: error: no valid servers configured
2016-01-06 16:04:04,683 ip-172-30-0-62 proftpd[8197]: Fatal: error processing configuration file '/etc/proftpd/proftpd.conf'
2016-01-06 16:04:08,674 ip-172-30-0-62 proftpd[8233]: warning: unable to determine IP address of 'ip-172-30-0-62'
2016-01-06 16:04:08,674 ip-172-30-0-62 proftpd[8233]: error: no valid servers configured
2016-01-06 16:04:08,674 ip-172-30-0-62 proftpd[8233]: Fatal: error processing configuration file '/etc/proftpd/proftpd.conf'

==> /var/log/supervisor/proftpd-stdout---supervisor-gzL8E4.log <==

Change then when to tags in https://github.com/ARTbio/ansible-artimed/blob/master/galaxy.yml to facilitate some tests.

Hi
Although I did tested this with the master branch, I think the issue will exist in the not yet merged dev branch:

On AWS, the ansible-mediated install works well. However if you shut down your instance and revive it, there is a number of errors arising from the change of the host IP, including for slurm daemon and other low level components of the artimed galaxy stuff.

It is not a terrible issue as you may associate a fixed IP to a new Amazon instance and keep it for months, but people with no experience in AWS model may be fucked the first time they use an instance of artimed.

Beyond the real issue is that - most probably - the same problem will arise is we share an ansible derived AMI (Image) ! Plus the fact that, even without understanding the details, I don't see why our ansible machines would need to know their host address: 127.0.0.1 should be enough should not it ?

On amazon worked previously, but now returns an error at bioblend call:

<localhost> ESTABLISH CONNECTION FOR USER: ubuntu
<localhost> REMOTE_MODULE command chdir=/tmp /tmp/venv/bin/python install_tool_shed_tools.py -t artimed_tool_list.yaml -a 379ab2a47d714a74b5cee4081703368e -g localhost:8080
<localhost> EXEC ssh -C -tt -vvv -o ControlMaster=auto -o ControlPersist=60s -o ControlPath="/home/ubuntu/.ansible/cp/ansible-ssh-%h-%p-%r" -o KbdInteractiveAuthentication=no -o PreferredAuthentications=gssapi-with-mic,gssapi-keyex,hostbased,publickey -o PasswordAuthentication=no -o ConnectTimeout=10 localhost /bin/sh -c 'mkdir -p $HOME/.ansible/tmp/ansible-tmp-1447548231.98-137057414169827 && chmod a+rx $HOME/.ansible/tmp/ansible-tmp-1447548231.98-137057414169827 && echo $HOME/.ansible/tmp/ansible-tmp-1447548231.98-137057414169827'
<localhost> PUT /tmp/tmpp7k0pI TO /home/ubuntu/.ansible/tmp/ansible-tmp-1447548231.98-137057414169827/command
<localhost> EXEC ssh -C -tt -vvv -o ControlMaster=auto -o ControlPersist=60s -o ControlPath="/home/ubuntu/.ansible/cp/ansible-ssh-%h-%p-%r" -o KbdInteractiveAuthentication=no -o PreferredAuthentications=gssapi-with-mic,gssapi-keyex,hostbased,publickey -o PasswordAuthentication=no -o ConnectTimeout=10 localhost /bin/sh -c 'sudo -k && sudo -H -S -p "[sudo via ansible, key=rqxkpgimyaqljdhfueqyuijhdwhjopyi] password: " -u root /bin/sh -c '"'"'echo BECOME-SUCCESS-rqxkpgimyaqljdhfueqyuijhdwhjopyi; LANG=C LC_CTYPE=C /usr/bin/python /home/ubuntu/.ansible/tmp/ansible-tmp-1447548231.98-137057414169827/command; rm -rf /home/ubuntu/.ansible/tmp/ansible-tmp-1447548231.98-137057414169827/ >/dev/null 2>&1'"'"''
failed: [localhost] => (item=artimed_tool_list.yaml) => {"changed": true, "cmd": ["/tmp/venv/bin/python", "install_tool_shed_tools.py", "-t", "artimed_tool_list.yaml", "-a", "379ab2a47d714a74b5cee4081703368e", "-g", "localhost:8080"], "delta": "0:00:00.111981", "end": "2015-11-15 00:43:52.171997", "item": "artimed_tool_list.yaml", "rc": 1, "start": "2015-11-15 00:43:52.060016", "warnings": []}
stderr: Traceback (most recent call last):
  File "install_tool_shed_tools.py", line 588, in <module>
    install_tools(options)
  File "install_tool_shed_tools.py", line 471, in install_tools
    itl = installed_tool_revisions(gi)  # installed tools list
  File "install_tool_shed_tools.py", line 170, in installed_tool_revisions
    itl = tsc.get_repositories()
  File "/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/toolshed/**init**.py", line 36, in get_repositories
    return Client._get(self)
  File "/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/client.py", line 147, in _get
    raise ConnectionError(msg)
bioblend.galaxy.client.ConnectionError: HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/tool_shed_repositories?key=379ab2a47d714a74b5cee4081703368e (Caused by NewConnectionError('<requests.packages.urllib3.connection.HTTPConnection object at 0x7f1b0cb45410>: Failed to establish a new connection: [Errno 111] Connection refused',)), 0 attempts left: None

FATAL: all hosts have already failed -- aborting

PLAY RECAP *******************************************************************\* 
           to retry, use: --limit @/home/ubuntu/tools.retry

localhost                  : ok=5    changed=4    unreachable=0    failed=1   ```

Similar to https://github.com/bgruening/docker-galaxy-stable/tree/master/galaxy
you should link your used roles into your repo, so that a simple vagrant up is enough to get going.

Nice work.
But please don't re-invent the wheel, you should include this for installing galaxy, slurm, database etc. pp.:
https://github.com/galaxyproject/usegalaxy-playbook

For an example of how it can be used look at this:
https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/Dockerfile

Specifically:

ansible-playbook /tmp/ansible/provision.yml \
    --extra-vars galaxy_user_name=$GALAXY_USER \
    --extra-vars galaxy_config_file=$GALAXY_CONFIG_FILE \
    --extra-vars galaxy_config_dir=$GALAXY_CONFIG_DIR \
    --extra-vars galaxy_job_conf_path=$GALAXY_CONFIG_JOB_CONFIG_FILE \
    --extra-vars galaxy_job_metrics_conf_path=$GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE \
    --extra-vars supervisor_manage_slurm="" \
    --tags=galaxyextras -c local && \

should replace the part where you clone and configure galaxy.
Good job, looks nice!

This is required to install the bowtie v1 data_manager, which is only available from the testtoolshed, for instance

Put here the roles that we needed to change and make sure we get this upstream if possible.

- ansible-galaxy-extras (pbkdf2 for admin, path to postgresql config file)

Include a custom welcome.html with a logo appropriate for the project.

Daemonize the install of Galaxy tools, so the user may leave the shell used to install galaxy. Also check if Galaxy is "on line" before start the Galaxy tools install.

Again, low priority.
Things like galaxy's config folder, the postgresql folder and the database folder should be stored
on the hosts file-system, so that re-creating the instance doesn't remove previous work.
You'd need a logic to detect whether you are at the first starrt of the instance or whether this data already exists. You can take hints from docker-galaxy-stable.

Well, the name says it all ;)
https://github.com/galaxyproject/ansible-galaxy-extras

This repo is where we should collect issues. Please push your branched/forked work that is ready for review here.

https://github.com/ARTbio/ansible-artimed/blob/master/README.md

Automatises the user creation in galaxy into a role.
Specifies a list of users to be create.
Use BioBlend to accomplish this.

Submodule path 'galaxy/roles/natefoo.postgresql_objects': checked out '81179c442016a1d5856d18252d89103a3da15be3'
ERROR: replace is not a legal parameter in an Ansible task or handler
Wait until galaxy provide the web service on http://localhost:8080
Press control+c to stop here or enter key to install Galaxy tools...

This is a milestone 0.2 issue, technically easy to do using bioblend,
but it should be reasonable for artimed. I might do this in the context of my own paper.
I propose to put a .ga file into extra-files, that will be referenced in in group_vars/artimed.
Importantly, the workflow needs to have a tool_list file associated to it.

@fabiorjvieira @drosofff
A suggestion to kickstart the project:
https://github.com/William-Yeh/docker-ansible

That way you would use the ansible role within docker, where the requirements are always the same
(I understand a lot of trouble comes from vagrant being different from amazon AMIs from local installs?!).
Then you build the image, you publish to dockerhub, and to test the image you would only need to do docker run artimed. It's almost no extra work and you can reproduce the problems easily.

Fix the bootstrap procedure in https://github.com/galaxyproject/ansible-galaxy-tools, so it can be used to create a temporary user to execute some data managers. The procedure must not interfere with the users already specified as admins in the galaxy configuration file (config/galaxy.ini).

to make the usage as simple as possible.

in https://github.com/ARTbio/ansible-artimed/blob/master/README.md#ansible-galaxy-instance-and-ngs-tools

a short description of what will happen is lacking.
basically:

• installation of a galaxy server in a /home/galaxy/galaxy dir
• customization of the web front page
• etc..
• saying that galaxy will work with slurm, 2 job handlers
• saying that galaxy will be controlled with supervisor/ctl galaxy: group

by the way what is the password if any of the galaxy account created by ansible.

It will be nice to have all this kind of information without need to know how to read a playbook. After all, the galaxy server does not know how it was spin on, and potential admin do not necessarily need to know it too.
Plus, this type of information will be require in an application note.

In https://github.com/fabiorjvieira/old-ansible-galaxy/blob/dev/galaxy.yml we build the message with the variable galaxy_hostname instead of the public ip or name of the machine.

So what we can directly access the running galaxy.

@fabiorjvieira you showed me an ansible install in a docker instance. Could you mention which branch of the repo was used to get this running ?

Galaxy handlers are configured in ports 8080 and 8081 (I already tested with ports 9080 and 9081).
But some thing is missing in NGINX config file to get this to handlers into consideration, because NGINX is not providing Galaxy in port 80. The playbook is https://github.com/ARTbio/ansible-artimed/blob/dev/galaxy/galaxy.yml and the procedure to install is described in https://github.com/ARTbio/ansible-artimed/blob/dev/README.md. I am currently comparing the installation config files with mississippi to se the difference and what is missing.

See discussion in https://github.com/ARTbio/internals/pull/12
I am not speaking of a new ansible driven installation. I am speaking of the case you raise a Galaxy amazon instance using ansible-artimed, then you snapshot an AMI, make it public, and propose people to redeploy is on their own, without replaying any playbook (even without knowing HOW the galaxy server was designed)

I will test this when possible

On my amazon instance, after installing git and openssh-client with apt-get install
creating the install.sh file and bash install.sh, I get:

PLAY [all] ******************************************************************** 

GATHERING FACTS *************************************************************** 
<localhost> ESTABLISH CONNECTION FOR USER: root
<localhost> REMOTE_MODULE setup
<localhost> EXEC ssh -C -tt -vvv -o ControlMaster=auto -o ControlPersist=60s -o ControlPath="/home/ubuntu/.ansible/cp/ansible-ssh-%h-%p-%r" -o KbdInteractiveAuthentication=no -o PreferredAuthentications=gssapi-with-mic,gssapi-keyex,hostbased,publickey -o PasswordAuthentication=no -o ConnectTimeout=10 localhost /bin/sh -c 'mkdir -p $HOME/.ansible/tmp/ansible-tmp-1446669386.23-177709563259750 && echo $HOME/.ansible/tmp/ansible-tmp-1446669386.23-177709563259750'
EXEC previous known host file not found for localhost
The authenticity of host 'localhost (127.0.0.1)' can't be established.
ECDSA key fingerprint is 06:fc:8c:d1:18:3b:50:e4:a3:63:6e:42:3d:40:84:71.
Are you sure you want to continue connecting (yes/no)? yes
fatal: [localhost] => SSH Error: Permission denied (publickey).
    while connecting to 127.0.0.1:22
It is sometimes useful to re-run the command using -vvvv, which prints SSH debug output to help diagnose the issue.

TASK: [galaxyprojectdotorg.galaxy-os | Add custom Galaxy PPA (used for nginx package)] *** 
FATAL: no hosts matched or all hosts have already failed -- aborting


PLAY RECAP ******************************************************************** 
           to retry, use: --limit @/home/ubuntu/galaxy.retry

localhost                  : ok=0    changed=0    unreachable=1    failed=0   

Wait until galaxy provide the web service on http://localhost:8080
Press control+c to stop here or enter key to install Galaxy tools...

Currently a password has to be set for connecting to postgresql, else proftpd can't communicate with the database to check a galaxy user's email and password.

Edit: We should move this away from my personal account.

As discussed with @drosofff, it's a good idea to have the external roles as backup, in case they disappear.

I'll do it manually for now, and then we could use a crontab to keep this up-to-date.

This one should be low-priority, but a simple Dockerfile with ansible would be enough
to clone this repo and setup the artimed instance. Nice for quick bugfixing :)

FROM ubuntu/14.04

RUN apt-get update && apt-get install build-essentials ansible
ADD galaxy.yml /galaxy.yml
RUN ansible-playbook galaxy.yml

Obvisouly I didn't test this, but it should be very easy with good ansible roles and playbooks :).

The galaxy mercurial repo is not properly maintained anymore.
Please use git and checkout a release branch, or directly download a zip of the code.