Galaxy NGS not displaying installed tools - bioinformatics

I'm running an instance of Galaxy NGS in an Ubuntu server, with a basic configuration, postgresql database, and apache.
When I log in as Admin in the Galaxy interface, and try to add a new tool through the tool shed, the tool is installed and I can use it without problems
However, if Galaxy needs to be restarted, the tool does not appear anymore
I followed the instructions here to configure a folder to keep the installed tools, like it explains there, adding a line in config.ini with the desired folder
tool_dependency_dir = dependency_dir
But that doesn't do the trick and the tools are not stored in the folder anyway
Does somebody have a clue on what could I be missing?

The problem was solved after switching from apache to nginx, and changing the line I posted to
tool_dependency_dir = /home/galaxy/tool_deps
I found a nice resource that helped me with the configuration in case somebody faces the same issue.
https://wiki.galaxyproject.org/Events/BioITWorld2014/W14#Setting_up_a_Local_Galaxy_Tutorial_.28Part_I.29

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I've just installed Elasticsearch and Kibana's latest versions (same versions) on Windows. When I launch Elasticsearch it starts just as normal and I can check through the browser that it's on the required port. But when I launch Kibana it gives me the error "\config was unexpected". I checked the configurations and made sure that Kibana knew where to connect to ES and tried re-installs but nothing changed. When I tried it on an Ubuntu virtual machine the two worked normally. I don't know where the issue is. Hope someone can help.
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I solved the problem. I'll just leave this for future reference:
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What solved this for me was simply to change the path of the Kibana directory. Apparently Windows had some trouble reading its own default name for the parent directory. Moving the kibana folder to a simpler directory (like C:) and even renaming the folder to simply "kibana" instead of including the version etc. made it run as normal.

composer windows vs ubuntu

Good evening,
This question is has to do with the PHP composer packet management. I have installed in on our test environment (xampp) without any issues and have downloaded the necessary package without any problems (package name: mpdf). After I issue the command to get the package, the vendor package showed up as it should have and my project worked great.
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Sharing a Vagrant box

I have a new developer coming to work with me soon, and I'd like to make it as simple as possible for them to get a development environment set up.
I'm currently using a Vagrant (Laravel Homestead) box with about 15 domains set up, each with different configurations (different PHP versions etc), and I'd like to just share the existing box with them if possible.
Is it as simple setting up a repository with the VagrantFile, getting them to clone it and provision the box, or are there more steps involved?
Also, I've had to edit the MySQL configuration on the box, is there any way I can include these updates in what I share with them, or will they just need to reconfigure their own version manually?
Any advice appreciated.
Thanks
The easiest way to share the Homestead environment is to use the after.sh file to to perform any customization you may need beyond what Homestead gives you.
You can also copy your Homestead.yaml file to Homestead.yaml.example for the new coworker to easily copy and paste the sites & any other configuration changes.

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I'm new to DevOps and build/automation tools. I installed Apache Maven and Jenkins, but the Jenkins dashboard is not popping up. In other words, I should be seeing this:
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I found a similar question here, but I was unable to understand what to do: How to access Jenkins dashboard locally when it is installed on staging server?
From what I understand, I need to make Jenkins open up on a different port, but I'm not sure how to do this. I checked in services and I can confirm that Jenkins is in fact running.
Ok, so I figured it out, but I still don't understand what that Apache page is. For anyone wondering how to fix the issue with the dashboard not popping up:
STEP 1: I was exploring the installation directory and found a file called jenkins.xml with the line --httpPort=8080.
STEP 2: It wouldn't let me edit and save the file so I dragged it to my desktop where it let me make changes. I changed 8080 to 8082, saved, and then placed the file back in the installation directory.
STEP 3: I didn't notice any changes until I restarted the Jenkins service and it's showing the dashboard now.
I still would like to know what that "Apache 2 Ubuntu Default Page" is about.

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When I run a Windows Azure web role on my local developer fabric, I get the following error:
The current service model is out of sync. Make sure both the service configuration and definition files are valid.
One of my colleagues hit this issue and after a bit of playing about, the problem was that the two service configuration files (cloud and local) had a different number of Settings.
When he updated the configuration files so that they were in sync it all worked.
A tip would be to use the GUI in Visual Studio to add new settings to both at the same time. The GUI can be accessed by right clicking the web role and selection properties. This should open up a window. Click the Settings tab on the left.
For me, this was caused by my azure project having been copied from one PC to another (going from Win 7 to Win 8.1 in the process). I am using VS 2013 Community edition on both, but I had upgraded from Azure 2.4 on Win7 to Azure 2.5 on the Win 8.1 machine.
If you unload the azure project and edit the csproj file, you just need to make a small edit (e.g. adding a comment) and save it, so it re-writes itself. This fixed it in my case (where I'd spent ages checking for errors in the CSDEF and CSCFG files). Once I re-saved the csproj file, it worked fine.
This happened to me because one of my cloud configuration files (.cscfg) was missing some key-value pairs that were defined in ServiceDefinition.csdef.
Going over the files manually was a pain. There's an easy way to discover the descrepancies:
In the Solution Explorer, right-click one of the Roles that make up
your Cloud Service and click 'Properties' in the context menu.
The Role properties window will open up grey with an error message saying:
"Invalid Service Definition or service configuration. Please see the
Error List for more details".
Open the Error List window and in some cases you
should be able to see a list of the specific discrepancies, complete with file
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I followed all the answers here and it still didn't work
eventually I restarted Visual Studio and it worked.
I believe the solution was the combination of one or more of the answers here + restarting VS.
What worked for me was to:
Make sure the Cloud Services .cscfg and .Local.cscfg files were identical (unless you need your Local.cscfg to have some differences for debugging purposes),
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Close the project and delete its Cloud Services .ccproj.user file.
After reloading the project, all was well.
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If it occours and everything seems to be correct, instead of restarting visual studio, simply unload the azurecloud project (rightclick: unload proecjt
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<Setting name="Microsoft.WindowsAzure.Plugins.Diagnostics.ConnectionString" value="UseDevelopmentStorage=true" />
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For me, the issue turned out to be an inconsistency between the vmName value I had assigned to one of my roles in my various environments. I have a *.cscfg files for my development, test, and production environments. Each of these had a role definition that was supposed to be along the lines of
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My problem was incorrect certificate definition in csdef file.
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