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Merge pull request #5 from briandrawert/gmsh_and_gillespy

Bug fixes and adding ODE solver for GillesPy
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ahellander committed Sep 17, 2015
2 parents ae02099 + 542c9e4 commit aa006ee64472dda68204a86ca3b2e3d905428c61
Showing with 18 additions and 9 deletions.
  1. +18 −7 MolnsLib/installSoftware.py
  2. +0 −2 molns.py
@@ -46,7 +46,7 @@ class InstallSW:
# EC2/S3 and OpenStack APIs
"sudo pip install boto",
"sudo apt-get -y install pandoc",
# This set of packages is really only needed for OpenStack, but molnsutil uses them
# This set of packages is needed for OpenStack, as molnsutil uses them for hybrid cloud deployment
"sudo apt-get -y install libxml2-dev libxslt1-dev python-dev",
"sudo pip install python-novaclient",
"sudo easy_install -U pip",
@@ -79,13 +79,23 @@ class InstallSW:
### Simulation software related to pyurdme and StochSS
# Gillespy
[ "sudo rm -rf /usr/local/stochkit;sudo mkdir -p /usr/local/stochkit;sudo chown ubuntu /usr/local/stochkit",
"cd /usr/local/ && git clone https://github.com/StochSS/stochkit.git",
"cd /usr/local/stochkit && ./install.sh",
[ "sudo rm -rf /usr/local/StochKit;sudo mkdir -p /usr/local/StochKit;sudo chown ubuntu /usr/local/StochKit",
"cd /usr/local/ && git clone https://github.com/StochSS/stochkit.git StochKit",
"cd /usr/local/StochKit && ./install.sh",
"sudo rm -rf /usr/local/ode-1.0.2;sudo mkdir -p /usr/local/ode-1.0.2/;sudo chown ubuntu /usr/local/ode-1.0.2",
"wget https://github.com/StochSS/stochss/blob/master/ode-1.0.2.tgz?raw=true -q -O /tmp/ode.tgz",
"cd /usr/local/ && tar -xzf /tmp/ode.tgz",
"rm /tmp/ode.tgz",
"cd /usr/local/ode-1.0.2/cvodes/ && tar -xzf \"cvodes-2.7.0.tar.gz\"",
"cd /usr/local/ode-1.0.2/cvodes/cvodes-2.7.0/ && ./configure --prefix=\"/usr/local/ode-1.0.2/cvodes/cvodes-2.7.0/cvodes\" 1>stdout.log 2>stderr.log",
"cd /usr/local/ode-1.0.2/cvodes/cvodes-2.7.0/ && make 1>stdout.log 2>stderr.log",
"cd /usr/local/ode-1.0.2/cvodes/cvodes-2.7.0/ && make install 1>stdout.log 2>stderr.log",
"cd /usr/local/ode-1.0.2/ && STOCHKIT_HOME=/usr/local/StochKit/ STOCHKIT_ODE=/usr/local/ode-1.0.2/ make 1>stdout.log 2>stderr.log",
"sudo rm -rf /usr/local/gillespy;sudo mkdir -p /usr/local/gillespy;sudo chown ubuntu /usr/local/gillespy",
"cd /usr/local/ && git clone https://github.com/MOLNs/gillespy.git",
"cd /usr/local/gillespy && sudo STOCHKIT_HOME=/usr/local/stochkit/ python setup.py install"
"cd /usr/local/gillespy && sudo STOCHKIT_HOME=/usr/local/StochKit/ STOCHKIT_ODE_HOME=/usr/local/ode-1.0.2/ python setup.py install"
],
@@ -100,8 +110,7 @@ class InstallSW:
# pyurdme
[ "sudo rm -rf /usr/local/pyurdme;sudo mkdir -p /usr/local/pyurdme;sudo chown ubuntu /usr/local/pyurdme",
"cd /usr/local/ && git clone https://github.com/MOLNs/pyurdme.git",
"cd /usr/local/pyurdme && git checkout develop",
#"cd /usr/local/pyurdme && git checkout develop", # for development only
"cp /usr/local/pyurdme/pyurdme/data/three.js_templates/js/* .ipython/profile_default/static/custom/",
"source /usr/local/pyurdme/pyurdme_init && python -c 'import pyurdme'",
],
@@ -115,6 +124,8 @@ class InstallSW:
# Upgrade scipy from pip to get rid of super-annoying six.py bug on Trusty
"sudo apt-get -y remove python-scipy",
"sudo pip install scipy",
"sudo pip install jsonschema jsonpointer", #redo this install to be sure it has not been removed.
"sync", # This is critial for some infrastructures.
View
@@ -1454,8 +1454,6 @@ def run(self, args, config_dir=None):
Command('import',{'filename.json':None},
function=MOLNSProvider.provider_import),
]),
# Commands to interact with the instance DB
SubCommand('instancedb',[
Command('list', {},

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