wiki contributions: Admin/Config/ProFTPd_with_AD
by Eric Rasche
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I'd like to contribute what I've learnt today to this particular page.
As it is "locked", I am unsure how to contribute my information, so I'm
posting here in the hopes that someone with rights will update it.
Formatted in (pandoc compatible) Markdown for your ease.
# Configuring ProFTPD with OpenLDAP
I've found a set of working options for using ProFTPD with OpenLDAP
servers (instead of AD).
This configuration file can be modified and placed in
`/etc/proftpd/conf.d/galaxy.conf
Using the /conf.d/ directory, you can allow the ProFTPd to serve both
local users (with PAM authentication) in the main configuration file,
AND galaxy users on another port.
```
<VirtualHost xxx.yyy.zzz>
RequireValidShell off
User galaxy
Group galaxy
Umask 137 027
AllowOverwrite on
# Ensure auth is LDAP
AuthPAM off
AuthOrder mod_ldap.c
# Serve this VirtualHost on port 4000
Port 4000
# LDAP Bind information
LDAPServer ldaps://xxx.yyy.zzz/??sub
LDAPUsers "ou=People,dc=yyy,dc=zzz" "(uid=%u)"
LDAPAuthBinds on
# Force those numbers even if LDAP finds a valid UID/GID
LDAPDefaultUID 1003
LDAPDefaultGID 1003
LDAPForceDefaultUID on
LDAPForceDefaultGID on
# Please generate home dir with user/group rwx permissions.
Could probably be stricter
CreateHome on 770
LDAPGenerateHomedir on 770
# Force this homedir even if LDAP said something different
LDAPForceGeneratedHomedir on
LDAPGenerateHomedirPrefix
"/home/galaxy/galaxy/database/ftp/%u(a)cpt.tamu.edu"
# The username is already incorporated in the %u, use this or it
will get appended again
LDAPGenerateHomedirPrefixNoUsername on
TransferLog /var/log/proftpd/xfer-galaxy.log
# Cause every FTP user to be "jailed" (chrooted) into their home
directory
DefaultRoot
"/home/galaxy/galaxy/database/ftp/%u(a)cpt.tamu.edu"
# Allow users to resume interrupted uploads
AllowStoreRestart on
# I set these as my passive ports because I run a very strict
firewall. Change as needed
PassivePorts 49152 50000
</VirtualHost>
```
Notably, this configuration allows a galaxy virtualhost to coexist with
the normal FTP capabilities provided by ProFTPd, so users can still
access their home directories AND galaxy users can upload to galaxy.
Authentication can of course be changed to suit one's needs.
# TLS Configuration
If you're running the galaxy FTP portion under a VirtualHost, like
described above, you'll notice that TLS directives placed in the main
proftpd.conf file do not apply to VirtualHosts. As such, you can add a
section that looks like this to every VirtualHost that needs to be secured
```
<IfModule mod_tls.c>
TLSEngine on
TLSLog /var/log/proftpd/tls.galaxy.log
# Your cert and private key
TLSRSACertificateFile /etc/ssl/certs/my.crt
TLSRSACertificateKeyFile /etc/ssl/private/my.key
TLSCACertificateFile /etc/ssl/certs/ca.bundle
# I've found that this is required for FileZilla
TLSOptions NoCertRequest EnableDiags NoSessionReuseRequired
# Most clients won't be sending certs
TLSVerifyClient off
TLSRequired on
</IfModule>
```
Cheers,
Eric
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
esr(a)tamu.edu
rasche.eric(a)yandex.ru
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8 years, 6 months
reasonable linux box specs
by Andrew Norman
Hi all
I'd like to set up a local installation of Galaxy on a dedicated linux
machine. I've taken a look at the Galaxy "appliance", but since I'm the
only one in my lab who will be using it, it's outside my price range.
I'm going to be doing RNA seq read mapping and differential expression
analysis. Can anyone recommend some minimum specs for the machine? I
understand that more memory/cores will enable faster processing, but I'm
willing to wait overnight for results to save some cash. Any advice you
have about this will be helpful!
Thanks,
Andy
8 years, 6 months
how to add openstack in biocloudcentral ?
by Jennifer Jackson
Hello Zeeshan, Let's post this over to the proper list,
galaxy-dev(a)bx.psu.edu, and see if that helps.
You could also contact Brad, the git repository owner, directly about
questions that involve biocloud.
Best,
Jen
Galaxy team
http://wiki.galaxyproject.org/MailingLists#The_lists
On 11/15/13 5:24 AM, Zeeshan Ali Shah wrote:
> Hi,
> I followed the guide from https://github.com/chapmanb/biocloudcentraland
> managed to run locally, But only see AWS in combo box, How to add private
> Openstack in it?
>
> --
>
> Regards
>
> Zeeshan Ali Shah
> System Administrator - PDC HPC
> PhD researcher (IT security)
> Kungliga Tekniska Hogskolan
> +46 8 790 9115
> http://www.pdc.kth.se/members/zashah
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
> http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
8 years, 6 months
Setting a queue for torque submission
by Jennifer Jackson
Hello, I am going to move your question over to the
galaxt-dev(a)bx.psu.edu mailing list to give it better visibility to the
development/local install community.
http://wiki.galaxyproject.org/MailingLists#The_lists
I didn't find it over here already, but apologies if double posted.
Also, since I don't know the best answer, will let others jump in!
Best,
Jen
Galaxy team
On 11/14/13 6:35 AM, Xian Su wrote:
> Greetings
>
> I'm having a hard time getting job submission to work via torque.
> Posted below is the relevant part of my universe file and job_conf.xml.
>
> The main cause comes from our torque server requiring a queue to be
> requested. I can submit jobs just fine via job .sub files via command
> line using qsub -q M30
>
> Running jobs via webgui results in the following:
> galaxy.jobs.runners.pbs WARNING 2013-11-14 13:54:23,722 (28)
> pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all
> destinations
> galaxy.jobs.runners.pbs ERROR 2013-11-14 13:54:25,724 (28) All
> attempts to submit job failed
>
> On the torque server's pbs logs, I see the corresponding
> 11/14/2013 13:54:23;0080;PBS_Server.66159;Req;req_reject;Reject reply
> code=15039(No default queue specified MSG=requested queue not found),
> aux=0, type=QueueJob, from xians(a)podmt1-100-62.novalocal
>
> In my universe_wsgi.ini, I'm currently using the settings:
> start_job_runners = pbs
> default_cluster_job_runner = pbs:///-q M30 -l nodes=1:ppn=12/
> ^I mainly have no idea how to find the correct syntax for this pbs:///
>
> But when I comment out default_cluster_job_runner and instead
> uncomment the line for the following job conf, I get the same error:
> <?xml version="1.0"?>
> <job_conf>
> <plugins workers="4">
> <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner"/>
> <plugin id="pbs" type="runner"
> load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/>
> </plugins>
> <handlers default="handlers">
> <handler id="main" tags="handlers"/>
> </handlers>
> <destinations default="pbs">
> <destination id="local" runner="local"/>
> <destination id="pbs" runner="pbs" tags="mycluster">
> <param
> id="Resource_List">walltime=72:00:00,nodes=1:ppn=12</param>
> <param id="-q">M30</param>
> </destination>
> </destinations>
> <tools>
> <tool id="main" handler="main" destination="pbs"/>
> </tools>
> <limits>
> </limits>
> </job_conf>
>
> Thank you in advance for any help.
>
> Regards,
> Xian
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
> http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
8 years, 6 months
Re: [galaxy-dev] Galaxy environment on local resources
by John Chilton
I am responding to galaxy-dev because others may have better answers than me.
On Wed, Nov 13, 2013 at 9:38 PM, Alistair Chilcott
<Alistair.Chilcott(a)utas.edu.au> wrote:
> John,
>
> Thanks for the advice, a dose of realism is always useful. :D
>
> I suspect that our current installation is fiddly primarily because it has been built on top of a Linux distro that was not installed initially just for Galaxy.
> It is running SUSE which varies enough in its behaviour from UBUNTU or BioLinux to make the job of interpreting/implementing the various instructions for "how to setup/maintain" much more difficult.
>
> As I suspected a full blown private cloud is optimistic at best, the question still needed to be asked. I still need to come up with a solution of some kind for the researchers.
>
> If I could pick your brain for a few minutes .....
> In your experience:
> What is the best (easiest to setup and maintain) way to deploy a galaxy instance (including tools the NGS suite in particular) onto a local VM or physical host?
The easiest way to setup everything is probably BioLinux (which you
mention below). I am not sure if it results in the easiest maintenance
however.
There is not a turn key solution yet and with things like data
managers and the tool shed the Galaxy team is constantly trying to
make these things more automated. When I was working on the Galaxy-P
project I put together getgalaxyp.org/install.html which is a fairly
automated way to configure Galaxy-P environment on Ubuntu and CentOS -
dozens of OS packages, custom tools, etc... It was built on
CloudBIoLinux. This is a superset of Galaxy, so it could (and should)
be trimmed back for a genomics focused setup. This install wouldn't
include the data, nginx server, or Galaxy itself but all of this could
be added to the procedure - the recipes are available in CloudBioLinux
becuase CloudMan uses them. I just need to find a free day sometime to
put all the pieces together and document them.
> What Linux distribution (and version) is most compatible with galaxy?
My recommended stack would be Ubuntu / postgres / nginx. CloudMan runs
this stack and so you can always pop a cloud image and see what a
working configuration looks like, also the community will likely have
the most answers for the configuration as well. Also, even if you
don't use the automated configuration scripts in CloudBioLinux - you
can always look at them to see what to do as well.
There is also this: http://bioteam.net/slipstream/galaxy-edition/.
Hope this helps,
-John
>
>
>
>
> Regards,
>
> Alistair
>
>
>
>
> -----Original Message-----
> From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton
> Sent: Thursday, 14 November 2013 5:10 AM
> To: Alistair Chilcott
> Cc: Galaxy Dev
> Subject: Re: [galaxy-dev] Galaxy environment on local resources
>
> On Tue, Nov 12, 2013 at 1:41 AM, Alistair Chilcott <Alistair.Chilcott(a)utas.edu.au> wrote:
>> Hello all,
>>
>> Feel free to point it out if I have missed something obvious, I have done a fair bit of investigation and haven't quite found the solution yet.
>>
>> We have some hardware that has been around for a while for the purpose of processing Genetic data and other related tasks.
>> To this end Galaxy fits the bill nicely in that it enables researchers to analyse data without being Linux geeks.
>>
>> The problem I have is that while the hand built galaxy server (running on SUSE for historical reasons) we have works to a point it is difficult to maintain and installing new tools and reference genomes is fiddly at best given that our server doesn't conform to the way the instructions for other systems expect it to work.
>>
>> We have had success using Cloudman on AWS to run training on how to use galaxy, and I would like to know more about how to customise and instance to contain all of the tools (mostly the NGS tools) we need by default.
>>
>> Ultimately we wont be able to use AWS to process much of the "real" data we have, because of a need to keep the data we are processing in-house due to ethics agreements. Fortunately we do have access to a modest pool of hardware (which is about to get bigger) to implement some kind of private cloud solution.
>>
>> How would I go about setting up a "private cloud" version of the cloudman style "galaxy instance on demand" system where researchers can start an instance, have it connect to a shared storage volume and process some data then terminate the instance? And is this even the best way to go?
>>
>> I have found it should be possible to use the scripts to install and configure the galaxy instances but I have not found any information on how to setup the environment that is required to make this work as a private cloud.
>>
>> Conversely I have found information about some private cloud scenarios such as Eucalyptis, and OpenStack but have not been able to join the dots to determine how to and if I can make the cloudman/galaxy usecase work on it.
>
> I think the way to do this would be to setup OpenStack and then install and configure CloudMan on your OpenStack cloud. I am not aware of something like CloudMan that deploys Galaxy without an existing cloud infrastructure. I have done this to some extent, I have put together some (dated) scripts for bootstrapping CloudMan on OpenStack still used by my old employer (MSI):
>
> https://github.com/jmchilton/cloudman_openstack_bootstrap
>
> A more modern starting point would be to extend the CloudBioLinux deployer instructions and scripts targeting Amazon for OpenStack (this will require some (small?) development effort though):
>
> https://github.com/chapmanb/cloudbiolinux/blob/master/deploy/cloudman.md
>
> Either path will take a lot of sys-admin-y work though.
>
> I hope I don't get in trouble for saying this, but my personal opinion is you should not do this though :). If you consider managing Galaxy fiddly (a fair criticism) than redoing everything an a cloudy manner is going to be several orders of magnitude more fiddly and more work.
> I have deployed OpenStack and worked with others doing another deployment, it will take a good system administrator months of effort to do this well and then it will take some amount of her or his time each week ongoing to maintain that layer of the infrastructure. Then instead of installing and maintaining Galaxy, you will have to do that still but with the added complexity of CloudMan.
>
> CloudMan works well on Amazon because you have a corporation full of amazing engineers operating the infrastructure, you have Dannon and Enis doing a heroic job configuring Galaxy and CloudMan, and dozens of users find and reporting problems. Trying to replicate that all yourself is quite difficult...
>
>>
>> I should mention that I'm primarily a Windows Sys Admin (who dabbles in Linux) who is looking at this due to a lack of a dedicated Linux admin.
>
> This is going to require more than dabbling...
>
>>
>> At the end of the day I need to be able to setup this system and make it as low maintenance as possible whilst being useful and accessible to the researchers who aren't Linux admins.
>
> Ekkk....
>
>>
>> Any advice gratefully accepted.
>
> It is all going to be on Amazon someday, work to make that happen sooner?
>
> If you are more comfortable with Windows, you could buy some sort of VMware server solution and try to create a simple gold standard VMware image of something that just contains Galaxy and just spin up single instances on a per project basis. Ultimately though the easiest number of Galaxy instances to manage is 1 :).
>
> Sorry this e-mail is kind of pessimistic, hopefully more well adjusted people will respond with happier advice.
>
> -John
>
>>
>> Regards,
>>
>> Alistair
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this and other
>> Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
8 years, 6 months
Failed to generate job destination
by Björn Grüning
Hi,
anyone has seen the following bug in Galaxy November release?
galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job
destination
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line
311, in __check_if_ready_to_run
self.job_wrappers[job.id].job_destination
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
620, in job_destination
return self.job_runner_mapper.get_job_destination(self.params)
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line
163, in get_job_destination
self.__cache_job_destination( params )
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line
148, in __cache_job_destination
raw_job_destination =
self.job_wrapper.tool.get_job_destination( params )
AttributeError: 'NoneType' object has no attribute 'get_job_destination'
Thanks,
Bjoern
8 years, 6 months
LDAP user auth
by Jon Ambler
Good morning!
I am setting up a galaxy instance at our department and I was hoping to use our LDAP database to authenticate users to use galaxy,
So my questions are:
How would one tell galaxy to refer to the LDAP database?
Would this allow new users to be automatically created on first login?
Thanks! Sorry about the not-so-great-to-deal-with question, I have dug through a lot of forms and the galaxy pages and didn't get very far...
Love galaxy in general though, keep up the great work!
Cheers!
Jon
Jon Ambler
MSc Bioinformatics student
Bioinformatics and Computational Biology Unit
Department of Biochemistry
Tree Protection Co-operative Program (TPCP) Research Group
Forestry and Agricultural Biotechnology Institute (FABI)
University of Pretoria
8 years, 6 months
