jmchilton

<h3>Development Setup for MSI Software Accounting Webapp</h3>

<p>Setup RVM, used to manage your ruby environment.
</p>
<pre>
%\curl -L https://get.rvm.io | bash -s
</pre>

<p>Configure your current shell session to use RVM.</p>

jmchilton

<h3>Development Setup for MSI Software Accounting Webapp</h3>

<p>Setup RVM, used to manage your ruby environment.
</p>
<pre>
%\curl -L https://get.rvm.io | bash -s
</pre>

<p>Configure your current shell session to use RVM.</p>

jmchilton

Deploying Production Galaxy Environments with CloudBioLinux and CloudMan

Typically, CloudMan is used to spin up a dedicated Galaxy virtual cluster for a single user or small group on Amazon EC2. This document outlines methods for deploying customized Galaxy instances that are more suitable for production environments - these enhancements include enabling load balancing, external authentication, SSL, reporting, and taking advantage of external resources such as dedicated file and

jmchilton

% wget https://raw.github.com/felipec/git/fc/remote/hg/contrib/remote-helpers/git-remote-hg
% mv git-remote-hg /place/on/path
% git clone hg::https://bitbucket.org/galaxy/galaxy-central  

jmchilton

<display id="protvis_mzml" version="1.0.0" name="display with ProtVis">
    <dynamic_links from_file="tool-data/protk_display_site.txt" skip_startswith="#" id="0" name="0">
        <!-- Define parameters by column from file -->
        <dynamic_param name="site_id" value="0"/>
        <dynamic_param name="site_url" value="1"/>
        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
        <url target_frame="galaxy_main">${site_url}/init_url?url=${mzml_file.qp}&amp;type=mzml${peptide_param.value}${spectrum_param.value}</url>
        <param type="data" name="mzml_file" url="galaxy_${DATASET_HASH}.mzml" />
        <param type="template" name="peptide" allow_override="True" />
        <param type="template" name="peptide_param" strip="True">                                                                                                             

jmchilton

from scripts.db_shell import *
from galaxy.util.bunch import Bunch
from galaxy.security import GalaxyRBACAgent
bunch = Bunch( **globals() )
bunch.engine = engine
# model.flush() has been removed.
bunch.session = db_session
# For backward compatibility with "model.context.current"
bunch.context = db_session
security_agent = GalaxyRBACAgent( bunch )

jmchilton

diff --git a/cloudbio/galaxy/__init__.py b/cloudbio/galaxy/__init__.py
index 33e3e74..823e04c 100644
--- a/cloudbio/galaxy/__init__.py
+++ b/cloudbio/galaxy/__init__.py
@@ -367,6 +367,7 @@ def _install_nginx(env):
             run("wget %s" % url)
             run("tar xvzf %s" % os.path.split(url)[1])
             with cd("nginx-%s" % version):
+                run("patch -p1 < ../nginx_tcp_proxy_module/tcp.patch")
                 run("./configure --prefix=%s --with-ipv6 %s "

jmchilton

#!/bin/bash                                                                                                           

SOURCE="${BASH_SOURCE[0]}"
app_dir="$( dirname "$SOURCE" )"
while [ -h "$SOURCE" ]
do
  SOURCE="$(readlink "$SOURCE")"
  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
  app_dir="$( cd -P "$( dirname "$SOURCE"  )" && pwd )"
done

jmchilton

   while 1:
        # Watch in_folder, upload anything that shows up there to data library and get ldda,
        # invoke workflow, move file to out_folder.
        for fname in os.listdir(in_folder):
            fullpath = os.path.join(in_folder, fname)
            if os.path.isdir(fullpath) and directory_ready(fullpath):
                directory_files = [os.path.join(fullpath, subdir_fname) for subdir_fname in os.path.listdir(fullpath)]
                data = {}
                data['folder_id'] = library_folder_id
                data['file_type'] = 'auto'

jmchilton

#!/bin/bash

# Enhanced Linux MZmine startup script, works as symbolic link.


# The HEAP_SIZE variable defines the Java heap size in MB. 
# That is the total amount of memory available to MZmine 2.
# By default we set this to the half of the physical memory 
# size, but feel free to adjust according to your needs. 
HEAP_SIZE=`free -m | awk '/Mem:/ {print int($2 / 2)}'`