artbio / galaxykickstart Goto Github PK
View Code? Open in Web Editor NEWAnsible playbooks for Galaxy Server deployment
License: GNU General Public License v3.0
Ansible playbooks for Galaxy Server deployment
License: GNU General Public License v3.0
Since the clinicians are probably only working with human data.
This repo is where we should collect issues. Please push your branched/forked work that is ready for review here.
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.
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 ```
in the running instance, the prompt for user says something not appropriate: a name which is not a full name and a port 2121.
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.
in https://github.com/ARTbio/ansible-artimed/blob/master/galaxy/install.sh#L87
in seems that $USER will be empty by default, is it a bug or a feature ?
See discussion in https://github.com/ARTbio/internals/pull/12
I am not speaking of a new ansible driven installation. I am speaking of the case you raise a Galaxy amazon instance using ansible-artimed, then you snapshot an AMI, make it public, and propose people to redeploy is on their own, without replaying any playbook (even without knowing HOW the galaxy server was designed)
I will test this when possible
Change then when to tags in https://github.com/ARTbio/ansible-artimed/blob/master/galaxy.yml to facilitate some tests.
Should be as simple as handling these variables:
galaxy_extras_config_ie_proxy: true
galaxy_extras_ie_fetch_ipython: false
galaxy_extras_ie_ipython_image: bgruening/docker-ipython-notebook:dev
galaxy_extras_ie_fetch_rstudio: false
galaxy_extras_ie_rstudio_image: erasche/docker-rstudio-notebook:dev
galaxy_docker_enabled: false
galaxy_docker_sudo: false
galaxy_docker_volumes_from: galaxy
galaxy_docker_volumes : "$defaults"
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/ansible-artimed/galaxy_vm$ bash install.sh
ubuntu@ip-172-30-0-137:
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
Get:1 http://us-east-1.ec2.archive.ubuntu.com trusty-updates InRelease [64.4 kB]
Hit http://us-east-1.ec2.archive.ubuntu.com trusty Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com trusty Release
Get:2 http://security.ubuntu.com trusty-security InRelease [64.4 kB]
Get:3 http://us-east-1.ec2.archive.ubuntu.com trusty-updates/main Sources [242 kB]
Get:4 http://us-east-1.ec2.archive.ubuntu.com trusty-updates/universe Sources [143 kB]
Get:5 http://us-east-1.ec2.archive.ubuntu.com trusty-updates/main amd64 Packages [638 kB]
Get:6 http://us-east-1.ec2.archive.ubuntu.com trusty-updates/universe amd64 Packages [326 kB]
Get:7 http://us-east-1.ec2.archive.ubuntu.com trusty-updates/main Translation-en [309 kB]
Get:8 http://us-east-1.ec2.archive.ubuntu.com trusty-updates/universe Translation-en [172 kB]
Get:9 http://security.ubuntu.com trusty-security/main Sources [98.0 kB]
Get:10 http://us-east-1.ec2.archive.ubuntu.com trusty/main Sources [1,064 kB]
Get:11 http://security.ubuntu.com trusty-security/universe Sources [31.0 kB]
Get:12 http://us-east-1.ec2.archive.ubuntu.com trusty/universe Sources [6,399 kB]
Get:13 http://security.ubuntu.com trusty-security/main amd64 Packages [357 kB]
Get:14 http://ppa.launchpad.net trusty InRelease [16.0 kB]
Get:15 http://security.ubuntu.com trusty-security/universe amd64 Packages [117 kB]
Hit http://us-east-1.ec2.archive.ubuntu.com trusty/main amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com trusty/universe amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com trusty/main Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com trusty/universe Translation-en
Ign http://us-east-1.ec2.archive.ubuntu.com trusty/main Translation-en_US
Ign http://us-east-1.ec2.archive.ubuntu.com trusty/universe Translation-en_US
Get:16 http://ppa.launchpad.net trusty/main amd64 Packages [493 B]
Get:17 http://security.ubuntu.com trusty-security/main Translation-en [194 kB]
Get:18 http://ppa.launchpad.net trusty/main Translation-en [322 B]
Get:19 http://security.ubuntu.com trusty-security/universe Translation-en [68.4 kB]
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.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main gcc-4.8-base amd64 4.8.4-2ubuntu114.04 [15.9 kB]14.04 [259 kB]
Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libstdc++6 amd64 4.8.4-2ubuntu1
Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libasan0 amd64 4.8.4-2ubuntu114.04 [63.0 kB]14.04 [8,650 B]
Get:4 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libatomic1 amd64 4.8.4-2ubuntu1
Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libgmp10 amd64 2:5.1.3+dfsg-1ubuntu1 [218 kB]
Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libisl10 amd64 0.12.2-1 [419 kB]
Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libcloog-isl4 amd64 0.18.2-1 [57.5 kB]
Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libgomp1 amd64 4.8.4-2ubuntu114.04 [23.1 kB]14.04 [28.6 kB]
Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libitm1 amd64 4.8.4-2ubuntu1
Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libmpfr4 amd64 3.1.2-1 [203 kB]
Get:11 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python2.7 amd64 2.7.6-8ubuntu0.2 [196 kB]
Get:12 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python2.7-minimal amd64 2.7.6-8ubuntu0.2 [1,185 kB]
Get:13 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libpython2.7 amd64 2.7.6-8ubuntu0.2 [1,039 kB]
Get:14 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libpython2.7-stdlib amd64 2.7.6-8ubuntu0.2 [1,869 kB]
Get:15 http://ppa.launchpad.net/ansible/ansible/ubuntu/ trusty/main ansible all 1.9.4-1ppatrusty [633 kB]14.04 [126 kB]
Get:16 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libpython2.7-minimal amd64 2.7.6-8ubuntu0.2 [308 kB]
Get:17 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libquadmath0 amd64 4.8.4-2ubuntu1
Get:18 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libtsan0 amd64 4.8.4-2ubuntu114.04 [94.7 kB]14.04 [4,597 kB]
Get:19 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libmpc3 amd64 1.0.1-1ubuntu1 [38.4 kB]
Get:20 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe python-support all 1.0.15 [26.7 kB]
Get:21 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main python-markupsafe amd64 0.18-1build2 [14.3 kB]
Get:22 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main python-jinja2 all 2.7.2-2 [161 kB]
Get:23 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main python-crypto amd64 2.6.1-4build1 [239 kB]
Get:24 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main python-paramiko all 1.10.1-1git1build1 [106 kB]
Get:25 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main python-httplib2 all 0.8-2build1 [35.4 kB]
Get:26 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe sshpass amd64 1.05-1 [10.5 kB]
Get:27 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main binutils amd64 2.24-5ubuntu14 [2,076 kB]
Get:28 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libc-dev-bin amd64 2.19-0ubuntu6.6 [68.9 kB]
Get:29 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main linux-libc-dev amd64 3.13.0-66.108 [775 kB]
Get:30 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libc6-dev amd64 2.19-0ubuntu6.6 [1,910 kB]
Get:31 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main cpp-4.8 amd64 4.8.4-2ubuntu1
Get:32 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main cpp amd64 4:4.8.2-1ubuntu6 [27.5 kB]
Get:33 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libgcc-4.8-dev amd64 4.8.4-2ubuntu114.04 [1,687 kB]14.04 [5,049 kB]
Get:34 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main gcc-4.8 amd64 4.8.4-2ubuntu1
Get:35 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main gcc amd64 4:4.8.2-1ubuntu6 [5,098 B]
Get:36 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libstdc++-4.8-dev amd64 4.8.4-2ubuntu114.04 [1,052 kB]14.04 [15.0 MB]
Get:37 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main g++-4.8 amd64 4.8.4-2ubuntu1
Get:38 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main g++ amd64 4:4.8.2-1ubuntu6 [1,490 B]
Get:39 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main make amd64 3.81-8.2ubuntu3 [119 kB]
Get:40 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main libdpkg-perl all 1.17.5ubuntu5.4 [179 kB]
Get:41 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main dpkg-dev all 1.17.5ubuntu5.4 [726 kB]
Get:42 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main build-essential amd64 11.6ubuntu6 [4,838 B]
Get:43 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libfakeroot amd64 1.20-3ubuntu2 [25.4 kB]
Get:44 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main fakeroot amd64 1.20-3ubuntu2 [55.0 kB]
Get:45 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-diff-perl all 1.19.02-3 [50.0 kB]
Get:46 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-diff-xs-perl amd64 0.04-2build4 [12.6 kB]
Get:47 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-merge-perl all 0.08-2 [12.7 kB]
Get:48 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main libfile-fcntllock-perl amd64 0.14-2build1 [15.9 kB]
Get:49 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/main manpages-dev all 3.54-1ubuntu1 [1,820 kB]
Get:50 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python3-pkg-resources all 3.3-1ubuntu2 [31.7 kB]
Get:51 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-chardet-whl all 2.2.1-2ubuntu1 [170 kB]ubuntu1 [83.5 kB]
Get:52 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-colorama all 0.2.5-0.1ubuntu2 [18.4 kB]
Get:53 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-colorama-whl all 0.2.5-0.1ubuntu2 [18.2 kB]
Get:54 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-distlib all 0.1.8-1ubuntu1 [113 kB]
Get:55 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-distlib-whl all 0.1.8-1ubuntu1 [140 kB]
Get:56 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-html5lib all 0.999-3
Get:57 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-html5lib-whl all 0.999-3ubuntu1 [109 kB]ubuntu1 [44.7 kB]
Get:58 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-six-whl all 1.5.2-1ubuntu1 [10.5 kB]
Get:59 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-urllib3-whl all 1.7.1-1ubuntu4 [64.0 kB]
Get:60 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-requests-whl all 2.2.1-1ubuntu0.3 [227 kB]
Get:61 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-setuptools-whl all 3.3-1ubuntu2 [244 kB]
Get:62 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-pip-whl all 1.5.4-1ubuntu3 [111 kB]
Get:63 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-pkg-resources all 3.3-1ubuntu2 [61.9 kB]
Get:64 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-setuptools all 3.3-1ubuntu2 [230 kB]
Get:65 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/universe python-pip all 1.5.4-1ubuntu3 [97.2 kB]
Get:66 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe python-virtualenv all 1.11.4-1 [1,485 kB]
Get:67 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python-wheel all 0.24.0-1
Get:68 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main software-properties-common all 0.92.37.5 [9,370 B]
Get:69 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty-updates/main python3-software-properties all 0.92.37.5 [19.1 kB]
Fetched 45.9 MB in 1s (38.2 MB/s)
Extracting templates from packages: 100%
(Reading database ... 51868 files and directories currently installed.)
Preparing to unpack .../gcc-4.8-base_4.8.4-2ubuntu114.04_amd64.deb ...14.04) over (4.8.2-19ubuntu1) ...
Unpacking gcc-4.8-base:amd64 (4.8.4-2ubuntu1
Setting up gcc-4.8-base:amd64 (4.8.4-2ubuntu114.04) ...14.04_amd64.deb ...
(Reading database ... 51868 files and directories currently installed.)
Preparing to unpack .../libstdc++6_4.8.4-2ubuntu1
Unpacking libstdc++6:amd64 (4.8.4-2ubuntu114.04) over (4.8.2-19ubuntu1) ...14.04) ...
Setting up libstdc++6:amd64 (4.8.4-2ubuntu1
Processing triggers for libc-bin (2.19-0ubuntu6.6) ...
Selecting previously unselected package libasan0:amd64.
(Reading database ... 51881 files and directories currently installed.)
Preparing to unpack .../libasan0_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libasan0:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package libatomic1:amd64.
Preparing to unpack .../libatomic1_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libatomic1:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package libgmp10:amd64.
Preparing to unpack .../libgmp10_2%3a5.1.3+dfsg-1ubuntu1_amd64.deb ...
Unpacking libgmp10:amd64 (2:5.1.3+dfsg-1ubuntu1) ...
Selecting previously unselected package libisl10:amd64.
Preparing to unpack .../libisl10_0.12.2-1_amd64.deb ...
Unpacking libisl10:amd64 (0.12.2-1) ...
Selecting previously unselected package libcloog-isl4:amd64.
Preparing to unpack .../libcloog-isl4_0.18.2-1_amd64.deb ...
Unpacking libcloog-isl4:amd64 (0.18.2-1) ...
Selecting previously unselected package libgomp1:amd64.
Preparing to unpack .../libgomp1_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libgomp1:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package libitm1:amd64.
Preparing to unpack .../libitm1_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libitm1:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package libmpfr4:amd64.
Preparing to unpack .../libmpfr4_3.1.2-1_amd64.deb ...
Unpacking libmpfr4:amd64 (3.1.2-1) ...
Preparing to unpack .../python2.7_2.7.6-8ubuntu0.2_amd64.deb ...
Unpacking python2.7 (2.7.6-8ubuntu0.2) over (2.7.6-8) ...
Preparing to unpack .../python2.7-minimal_2.7.6-8ubuntu0.2_amd64.deb ...
Unpacking python2.7-minimal (2.7.6-8ubuntu0.2) over (2.7.6-8) ...
Preparing to unpack .../libpython2.7_2.7.6-8ubuntu0.2_amd64.deb ...
Unpacking libpython2.7:amd64 (2.7.6-8ubuntu0.2) over (2.7.6-8) ...
Preparing to unpack .../libpython2.7-stdlib_2.7.6-8ubuntu0.2_amd64.deb ...
Unpacking libpython2.7-stdlib:amd64 (2.7.6-8ubuntu0.2) over (2.7.6-8) ...
Preparing to unpack .../libpython2.7-minimal_2.7.6-8ubuntu0.2_amd64.deb ...
Unpacking libpython2.7-minimal:amd64 (2.7.6-8ubuntu0.2) over (2.7.6-8) ...
Selecting previously unselected package libquadmath0:amd64.
Preparing to unpack .../libquadmath0_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libquadmath0:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package libtsan0:amd64.
Preparing to unpack .../libtsan0_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libtsan0:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package libmpc3:amd64.
Preparing to unpack .../libmpc3_1.0.1-1ubuntu1_amd64.deb ...
Unpacking libmpc3:amd64 (1.0.1-1ubuntu1) ...
Selecting previously unselected package python-support.
Preparing to unpack .../python-support_1.0.15_all.deb ...
Unpacking python-support (1.0.15) ...
Selecting previously unselected package python-markupsafe.
Preparing to unpack .../python-markupsafe_0.18-1build2_amd64.deb ...
Unpacking python-markupsafe (0.18-1build2) ...
Selecting previously unselected package python-jinja2.
Preparing to unpack .../python-jinja2_2.7.2-2_all.deb ...
Unpacking python-jinja2 (2.7.2-2) ...
Selecting previously unselected package python-crypto.
Preparing to unpack .../python-crypto_2.6.1-4build1_amd64.deb ...
Unpacking python-crypto (2.6.1-4build1) ...
Selecting previously unselected package python-paramiko.
Preparing to unpack .../python-paramiko_1.10.1-1git1build1_all.deb ...
Unpacking python-paramiko (1.10.1-1git1build1) ...
Selecting previously unselected package python-httplib2.
Preparing to unpack .../python-httplib2_0.8-2build1_all.deb ...
Unpacking python-httplib2 (0.8-2build1) ...
Selecting previously unselected package sshpass.
Preparing to unpack .../sshpass_1.05-1_amd64.deb ...
Unpacking sshpass (1.05-1) ...
Selecting previously unselected package ansible.
Preparing to unpack .../ansible_1.9.4-1ppatrusty_all.deb ...trusty) ...
Unpacking ansible (1.9.4-1ppa
Selecting previously unselected package binutils.
Preparing to unpack .../binutils_2.24-5ubuntu14_amd64.deb ...
Unpacking binutils (2.24-5ubuntu14) ...
Selecting previously unselected package libc-dev-bin.
Preparing to unpack .../libc-dev-bin_2.19-0ubuntu6.6_amd64.deb ...
Unpacking libc-dev-bin (2.19-0ubuntu6.6) ...
Selecting previously unselected package linux-libc-dev:amd64.
Preparing to unpack .../linux-libc-dev_3.13.0-66.108_amd64.deb ...
Unpacking linux-libc-dev:amd64 (3.13.0-66.108) ...
Selecting previously unselected package libc6-dev:amd64.
Preparing to unpack .../libc6-dev_2.19-0ubuntu6.6_amd64.deb ...
Unpacking libc6-dev:amd64 (2.19-0ubuntu6.6) ...
Selecting previously unselected package cpp-4.8.
Preparing to unpack .../cpp-4.8_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking cpp-4.8 (4.8.4-2ubuntu1
Selecting previously unselected package cpp.
Preparing to unpack .../cpp_4%3a4.8.2-1ubuntu6_amd64.deb ...
Unpacking cpp (4:4.8.2-1ubuntu6) ...
Selecting previously unselected package libgcc-4.8-dev:amd64.
Preparing to unpack .../libgcc-4.8-dev_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libgcc-4.8-dev:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package gcc-4.8.
Preparing to unpack .../gcc-4.8_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking gcc-4.8 (4.8.4-2ubuntu1
Selecting previously unselected package gcc.
Preparing to unpack .../gcc_4%3a4.8.2-1ubuntu6_amd64.deb ...
Unpacking gcc (4:4.8.2-1ubuntu6) ...
Selecting previously unselected package libstdc++-4.8-dev:amd64.
Preparing to unpack .../libstdc++-4.8-dev_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking libstdc++-4.8-dev:amd64 (4.8.4-2ubuntu1
Selecting previously unselected package g++-4.8.
Preparing to unpack .../g++-4.8_4.8.4-2ubuntu114.04_amd64.deb ...14.04) ...
Unpacking g++-4.8 (4.8.4-2ubuntu1
Selecting previously unselected package g++.
Preparing to unpack .../g++_4%3a4.8.2-1ubuntu6_amd64.deb ...
Unpacking g++ (4:4.8.2-1ubuntu6) ...
Selecting previously unselected package make.
Preparing to unpack .../make_3.81-8.2ubuntu3_amd64.deb ...
Unpacking make (3.81-8.2ubuntu3) ...
Selecting previously unselected package libdpkg-perl.
Preparing to unpack .../libdpkg-perl_1.17.5ubuntu5.4_all.deb ...
Unpacking libdpkg-perl (1.17.5ubuntu5.4) ...
Selecting previously unselected package dpkg-dev.
Preparing to unpack .../dpkg-dev_1.17.5ubuntu5.4_all.deb ...
Unpacking dpkg-dev (1.17.5ubuntu5.4) ...
Selecting previously unselected package build-essential.
Preparing to unpack .../build-essential_11.6ubuntu6_amd64.deb ...
Unpacking build-essential (11.6ubuntu6) ...
Selecting previously unselected package libfakeroot:amd64.
Preparing to unpack .../libfakeroot_1.20-3ubuntu2_amd64.deb ...
Unpacking libfakeroot:amd64 (1.20-3ubuntu2) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.20-3ubuntu2_amd64.deb ...
Unpacking fakeroot (1.20-3ubuntu2) ...
Selecting previously unselected package libalgorithm-diff-perl.
Preparing to unpack .../libalgorithm-diff-perl_1.19.02-3_all.deb ...
Unpacking libalgorithm-diff-perl (1.19.02-3) ...
Selecting previously unselected package libalgorithm-diff-xs-perl.
Preparing to unpack .../libalgorithm-diff-xs-perl_0.04-2build4_amd64.deb ...
Unpacking libalgorithm-diff-xs-perl (0.04-2build4) ...
Selecting previously unselected package libalgorithm-merge-perl.
Preparing to unpack .../libalgorithm-merge-perl_0.08-2_all.deb ...
Unpacking libalgorithm-merge-perl (0.08-2) ...
Selecting previously unselected package libfile-fcntllock-perl.
Preparing to unpack .../libfile-fcntllock-perl_0.14-2build1_amd64.deb ...
Unpacking libfile-fcntllock-perl (0.14-2build1) ...
Selecting previously unselected package manpages-dev.
Preparing to unpack .../manpages-dev_3.54-1ubuntu1_all.deb ...
Unpacking manpages-dev (3.54-1ubuntu1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../python3-pkg-resources_3.3-1ubuntu2_all.deb ...
Unpacking python3-pkg-resources (3.3-1ubuntu2) ...
Selecting previously unselected package python-chardet-whl.
Preparing to unpack .../python-chardet-whl_2.2.1-2ubuntu1_all.deb ...ubuntu1) ...
Unpacking python-chardet-whl (2.2.1-2
Selecting previously unselected package python-colorama.
Preparing to unpack .../python-colorama_0.2.5-0.1ubuntu2_all.deb ...
Unpacking python-colorama (0.2.5-0.1ubuntu2) ...
Selecting previously unselected package python-colorama-whl.
Preparing to unpack .../python-colorama-whl_0.2.5-0.1ubuntu2_all.deb ...
Unpacking python-colorama-whl (0.2.5-0.1ubuntu2) ...
Selecting previously unselected package python-distlib.
Preparing to unpack .../python-distlib_0.1.8-1ubuntu1_all.deb ...
Unpacking python-distlib (0.1.8-1ubuntu1) ...
Selecting previously unselected package python-distlib-whl.
Preparing to unpack .../python-distlib-whl_0.1.8-1ubuntu1_all.deb ...
Unpacking python-distlib-whl (0.1.8-1ubuntu1) ...
Selecting previously unselected package python-html5lib.
Preparing to unpack .../python-html5lib_0.999-3ubuntu1_all.deb ...ubuntu1) ...
Unpacking python-html5lib (0.999-3
Selecting previously unselected package python-html5lib-whl.
Preparing to unpack .../python-html5lib-whl_0.999-3ubuntu1_all.deb ...ubuntu1) ...
Unpacking python-html5lib-whl (0.999-3
Selecting previously unselected package python-six-whl.
Preparing to unpack .../python-six-whl_1.5.2-1ubuntu1_all.deb ...
Unpacking python-six-whl (1.5.2-1ubuntu1) ...
Selecting previously unselected package python-urllib3-whl.
Preparing to unpack .../python-urllib3-whl_1.7.1-1ubuntu4_all.deb ...
Unpacking python-urllib3-whl (1.7.1-1ubuntu4) ...
Selecting previously unselected package python-requests-whl.
Preparing to unpack .../python-requests-whl_2.2.1-1ubuntu0.3_all.deb ...
Unpacking python-requests-whl (2.2.1-1ubuntu0.3) ...
Selecting previously unselected package python-setuptools-whl.
Preparing to unpack .../python-setuptools-whl_3.3-1ubuntu2_all.deb ...
Unpacking python-setuptools-whl (3.3-1ubuntu2) ...
Selecting previously unselected package python-pip-whl.
Preparing to unpack .../python-pip-whl_1.5.4-1ubuntu3_all.deb ...
Unpacking python-pip-whl (1.5.4-1ubuntu3) ...
Preparing to unpack .../python-pkg-resources_3.3-1ubuntu2_all.deb ...
Unpacking python-pkg-resources (3.3-1ubuntu2) over (3.3-1ubuntu1) ...
Selecting previously unselected package python-setuptools.
Preparing to unpack .../python-setuptools_3.3-1ubuntu2_all.deb ...
Unpacking python-setuptools (3.3-1ubuntu2) ...
Selecting previously unselected package python-pip.
Preparing to unpack .../python-pip_1.5.4-1ubuntu3_all.deb ...
Unpacking python-pip (1.5.4-1ubuntu3) ...
Selecting previously unselected package python-virtualenv.
Preparing to unpack .../python-virtualenv_1.11.4-1_all.deb ...
Unpacking python-virtualenv (1.11.4-1) ...
Selecting previously unselected package python-wheel.
Preparing to unpack .../python-wheel_0.24.0-1ubuntu1_all.deb ...ubuntu1) ...
Unpacking python-wheel (0.24.0-1
Preparing to unpack .../software-properties-common_0.92.37.5_all.deb ...
Unpacking software-properties-common (0.92.37.5) over (0.92.37.3) ...
Preparing to unpack .../python3-software-properties_0.92.37.5_all.deb ...
Unpacking python3-software-properties (0.92.37.5) over (0.92.37.3) ...
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Processing triggers for mime-support (3.54ubuntu1.1) ...
Setting up libasan0:amd64 (4.8.4-2ubuntu114.04) ...14.04) ...
Setting up libatomic1:amd64 (4.8.4-2ubuntu1
Setting up libgmp10:amd64 (2:5.1.3+dfsg-1ubuntu1) ...
Setting up libisl10:amd64 (0.12.2-1) ...
Setting up libcloog-isl4:amd64 (0.18.2-1) ...
Setting up libgomp1:amd64 (4.8.4-2ubuntu114.04) ...14.04) ...
Setting up libitm1:amd64 (4.8.4-2ubuntu1
Setting up libmpfr4:amd64 (3.1.2-1) ...
Setting up libpython2.7-minimal:amd64 (2.7.6-8ubuntu0.2) ...
Setting up python2.7-minimal (2.7.6-8ubuntu0.2) ...
Setting up libpython2.7-stdlib:amd64 (2.7.6-8ubuntu0.2) ...
Setting up python2.7 (2.7.6-8ubuntu0.2) ...
Setting up libpython2.7:amd64 (2.7.6-8ubuntu0.2) ...
Setting up libquadmath0:amd64 (4.8.4-2ubuntu114.04) ...14.04) ...
Setting up libtsan0:amd64 (4.8.4-2ubuntu1
Setting up libmpc3:amd64 (1.0.1-1ubuntu1) ...
Setting up python-support (1.0.15) ...
Setting up python-markupsafe (0.18-1build2) ...
Setting up python-jinja2 (2.7.2-2) ...
Setting up python-crypto (2.6.1-4build1) ...
Setting up python-paramiko (1.10.1-1git1build1) ...
Setting up python-httplib2 (0.8-2build1) ...
Setting up sshpass (1.05-1) ...
Setting up ansible (1.9.4-1ppatrusty) ...14.04) ...
Setting up binutils (2.24-5ubuntu14) ...
Setting up libc-dev-bin (2.19-0ubuntu6.6) ...
Setting up linux-libc-dev:amd64 (3.13.0-66.108) ...
Setting up libc6-dev:amd64 (2.19-0ubuntu6.6) ...
Setting up cpp-4.8 (4.8.4-2ubuntu1
Setting up cpp (4:4.8.2-1ubuntu6) ...
Setting up libgcc-4.8-dev:amd64 (4.8.4-2ubuntu114.04) ...14.04) ...
Setting up gcc-4.8 (4.8.4-2ubuntu1
Setting up gcc (4:4.8.2-1ubuntu6) ...
Setting up libstdc++-4.8-dev:amd64 (4.8.4-2ubuntu114.04) ...14.04) ...
Setting up g++-4.8 (4.8.4-2ubuntu1
Setting up g++ (4:4.8.2-1ubuntu6) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up make (3.81-8.2ubuntu3) ...
Setting up libdpkg-perl (1.17.5ubuntu5.4) ...
Setting up dpkg-dev (1.17.5ubuntu5.4) ...
Setting up build-essential (11.6ubuntu6) ...
Setting up libfakeroot:amd64 (1.20-3ubuntu2) ...
Setting up fakeroot (1.20-3ubuntu2) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up libalgorithm-diff-perl (1.19.02-3) ...
Setting up libalgorithm-diff-xs-perl (0.04-2build4) ...
Setting up libalgorithm-merge-perl (0.08-2) ...
Setting up libfile-fcntllock-perl (0.14-2build1) ...
Setting up manpages-dev (3.54-1ubuntu1) ...
Setting up python3-pkg-resources (3.3-1ubuntu2) ...
Setting up python-chardet-whl (2.2.1-2ubuntu1) ...ubuntu1) ...
Setting up python-colorama (0.2.5-0.1ubuntu2) ...
Setting up python-colorama-whl (0.2.5-0.1ubuntu2) ...
Setting up python-distlib (0.1.8-1ubuntu1) ...
Setting up python-distlib-whl (0.1.8-1ubuntu1) ...
Setting up python-html5lib (0.999-3
Setting up python-html5lib-whl (0.999-3ubuntu1) ...ubuntu1) ...
Setting up python-six-whl (1.5.2-1ubuntu1) ...
Setting up python-urllib3-whl (1.7.1-1ubuntu4) ...
Setting up python-requests-whl (2.2.1-1ubuntu0.3) ...
Setting up python-setuptools-whl (3.3-1ubuntu2) ...
Setting up python-pip-whl (1.5.4-1ubuntu3) ...
Setting up python-pkg-resources (3.3-1ubuntu2) ...
Setting up python-setuptools (3.3-1ubuntu2) ...
Setting up python-pip (1.5.4-1ubuntu3) ...
Setting up python-virtualenv (1.11.4-1) ...
Setting up python-wheel (0.24.0-1
Setting up python3-software-properties (0.92.37.5) ...
Setting up software-properties-common (0.92.37.5) ...
Processing triggers for libc-bin (2.19-0ubuntu6.6) ...
Processing triggers for python-support (1.0.15) ...
fatal: destination path '/home/ubuntu/ansible-artimed' already exists and is not an empty directory.
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
Showstoppers:
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 <==
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
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)
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.
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.
This is required to install the bowtie v1 data_manager, which is only available from the testtoolshed, for instance
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...
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).
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...
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.
@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.
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.
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
to make the usage as simple as possible.
Well, the name says it all ;)
https://github.com/galaxyproject/ansible-galaxy-extras
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.
@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.
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.
a short description of what will happen is lacking.
basically:
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.
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.
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...
@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 ?
Include a custom welcome.html with a logo appropriate for the project.
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
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 ?
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!
And deposit workflow in a repository.
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 :).
version d20e36a
seems a bit odd
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.
This is necessary for interacting with the api to install tools or workflows.
So what we can directly access the running galaxy.
Automatises the user creation in galaxy into a role.
Specifies a list of users to be create.
Use BioBlend to accomplish this.
@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 ?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.