jmchilton

import java.io.InputStream;
import java.lang.reflect.InvocationHandler;
import java.lang.reflect.Method;
import java.lang.reflect.Proxy;
import java.util.Properties;

import com.google.gwt.i18n.client.Constants;

public class ConstantProxies {

jmchilton

# Place this file (preseed.py) in your galaxy directory and run it via
# python preseed.py
from scripts.db_shell import *

admin_user = User("admin@localhost")
admin_user.set_password_cleartext("test1")
sa_session.add(admin_user)
sa_session.flush()

user = User("user@localhost")

jmchilton

  public Ratios computeRatios(final ITraqLabel numLabel, final ITraqLabel denLabel, final ReportSummary reportSummary,
      final Function<Double, Double> weightFunction) {
    final double[] ratios = new double[reportSummary.getNumProteins()], pValues = new double[reportSummary.getNumProteins()];
    int proteinNum = 0;
    for(final String protein : reportSummary.getProteins()) {
      final ProteinSummary proteinSummary = reportSummary.getProteinSummary(protein);
      final double[] iRatio = new double[proteinSummary.getNumEntries()];
      final double[] num = proteinSummary.getIntensities(numLabel);
      final double[] den = proteinSummary.getIntensities(denLabel);

jmchilton

# Using arrays
grep "identification.*user.*Running" sed_test | sed 's/[^\[]*\[\([\: 0-9\-]*\).*\jobName=\(.*\)\,jobId=\([0-9]*\).*/\1\t\3\t\2/' | awk 'BEGIN {i=0;lj=0} {if(lj!=$2) {i=i+1}; lj=$2; if(s[i]==""){s[i]=e[i]=$1;t[i]=$3}; e[i]=$1;} END{ print i;for(idx=1;idx<=i;idx++){ cmd="date --date=\"" s[idx] "\" +%s"; cmd | getline se; cmd="date --date=\"" e[idx] "\" +%s"; cmd | getline ee;  print  (ee - se) / 60, "\t" t[idx]}}' FS="\t"

# Improvement using hashs
grep "identification.*user.*Running" sed_test | sed 's/[^\[]*\[\([\: 0-9\-]*\).*\jobName=\(.*\)\,jobId=\([0-9]*\).*/\1\t\3\t\2/' | awk 'BEGIN {i=0;lj=0} {i=$2$3; lj=$2; if(s[i]==""){s[i]=e[i]=$1;t[i]=$3}; e[i]=$1;} END{ print i;for(idx in s){ cmd="date --date=\"" s[idx] "\" +%s"; cmd | getline se; cmd="date --date=\"" e[idx] "\" +%s"; cmd | getline ee;  print  (ee - se) / 60, "\t" t[idx]}}' FS="\t"

jmchilton

Obtaining Tools

Repositories for all Galaxy-P tools can be found at https:/bitbucket.org/galaxyp/.

Contact

Please send suggestions for improvements and bug reports to jmchilton@gmail.com.

jmchilton

import javax.net.ssl.HostnameVerifier;
import javax.net.ssl.SSLContext;
import javax.net.ssl.SSLSession;

import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
import com.sun.jersey.api.json.JSONConfiguration;
import com.sun.jersey.client.urlconnection.HTTPSProperties;

...

jmchilton

diff -r b2975e2fa684 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py	Fri Oct 26 12:56:23 2012 -0400
+++ b/lib/galaxy/jobs/handler.py	Wed Oct 31 12:00:10 2012 -0500
@@ -397,6 +397,11 @@
     def put( self, job_wrapper ):
         try:
             runner_name = self.__get_runner_name( job_wrapper )
+        except Exception:
+            log.exception( 'Failed to generate job runner name' )
+            job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system.  Please contact a site administrator.' )

jmchilton

diff -r ec3b5956130f lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py	Wed Oct 31 12:18:55 2012 -0500
+++ b/lib/galaxy/jobs/handler.py	Wed Oct 31 13:42:38 2012 -0500
@@ -17,6 +17,7 @@
 
 # States for running a job. These are NOT the same as data states
 JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_READY, JOB_DELETED, JOB_ADMIN_DELETED = 'wait', 'error', 'input_error', 'input_deleted', 'ready', 'deleted', 'admin_deleted'
+DEFAULT_JOB_PUT_FAILURE_MESSAGE = 'Unable to run job due to a misconfiguration of the Galaxy job running system.  Please contact a site administrator.'
 
 class JobHandler( object ):

jmchilton

<p>There are currently two software accounting databases. MSIdb contains the most up-to-date demographic, resource, and FLEXlm records but not collectl data. All collectl data is stored in an appdev managed database on appdev-dom0, the demographic, resource and FLEXlm records are occasionally copied over from MSIdb to appdev-dom0.</p>

<p>Both of these databases can be access from loon.msi.umn.edu. To access you will first need to create a .pgpass file in your home directory.</p>

<pre>
% touch $HOME/.pgpass; chmod 600 $HOME/.pgpass; cat /project/msistaff/appdev/softacct/PGPASS_EXAMPLE >> $HOME/.pgpass
</pre>

<p>Once your .pgpass file is setup, you can access the appdev-dom0 database from loon with the following command:</p>
<pre>

jmchilton

Galaxy Tool/Job Running:
---------------------

Entry points: 
lib/webapps/galaxy/controllers/tool_runner.py (method: index)
lib/webapps/galaxy/api/tools.py (method: create)

Generate tool from id. 

Setup params: