Re: [galaxy-dev] Advice on Galaxy administration

[Peter Cock]

On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan  wrote:
> Hi Peter,
>
>
> On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock  wrote:
>> Hi Ray,
>>
>> You will absolutely need command line access to the Galaxy
>> server for some of the administration tasks - the web admin
>> controls and web report tool only let you do some of the likely
>> tasks.
>>
>> During the initial setup admin (sudo) rights would be useful,
>> at very least you'll need the sys admin to help with mounting
>> shared network drives, cluster integration, database setup.
>> If you want to run cluster jobs as the associated Unix account
>> of each user, or anything like LDAP logins, then again you
>> will need help from your sys admin.
>
>
> I see!
>
> Sorry to go off on a tangent, but something I'm marginally familiar
> with is content management systems (CMS) such as Joomla and WordPress
> and maybe I can use it as an analogy to make sure I understand.  For
> those, suppose we create an account "ray" who owns or is in a group
> with the Apache process who owns:
>
> 1)  the directory that Joomla resides in and all subdirectories,
> 2)  is the database administrator of the MySQL database, and
> 3)  is the administrator of the Joomla web interface
>
> then I wouldn't need sudo access.  On occasion, the Apache
> configuration might need to be changed and the system administrator
> can be asked to do that, but that's probably once a year or something.
>
> Is Galaxy like this?  Or do you reckon I need full sudo access?
>
> Sorry, I just want to make sure when I ask for greater access, I have
> an idea how Galaxy works or how it might differ from a CMS.
>

There are certainly similarities with the CMS idea - Galaxy
also has its own user accounts, and interacts with Apache.

I would certainly opt for a galaxy Linux user account with
minimal rights (no sudo!), which would own all the files by
default, and also galaxy specific database accounts (probably
PostgreSQL not MySQL).

We then install various Galaxy specific dependencies like
samtools under $HOME/bin which is on the Galaxy user's
$PATH - which like the main Tool Shed dependency mechanism
installs tools locally without needing sys admin rights on the
Galaxy server or cluster.

When I have needed sudo has been during Galaxy setup
(often), but only occasionally since (e.g. debugging and
needing to restart services, or changing Apache settings).

Peter
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Re: [galaxy-dev] pbs_python can't be installed via scramble

[Will Holtz]

Here is an old thread that looks rather similar to your problems:
https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.html

-Will


On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis 
wrote:

> Hello everyone,
>
> I'm trying to set up a Galaxy instance on a multi-core server in my
> university so according to the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
>
> I installed Torque, changed the eggs.ini file by adding the 4.4.0. version
> of pbs_python
>
> and tried to setup pbs_python via scramble:
>
> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>
> When I did that I got the error:
>
> Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir
> via PBS_PYTHON_INCLUDEDIR variable)
> Traceback (most recent call last):
>   File "scripts/scramble.py", line 50, in 
> egg.scramble()
>   File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in
> scramble
> self.run_scramble_script()
>   File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in
> run_scramble_script
> raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % (
> sys._getframe().f_code.co_name, self.name, self.version ) )
> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
> failed for pbs_python 4.4.0
>
> so I did some digging around and found that the file I need is in
>
> /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
>
> (please correct me if I am wrong)
>
> So I tried again using:
>
>  
> PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>
> but then I got the error:
>
> In file included from src/C++/pbs_ifl.h:90:0,
>  from src/C++/pbs_wrap.cxx:2978:
> /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp:
> No such file or directory
>  #include "container.hpp"
>
>
> Can someone help me please?
>
> Kind regards,
> Makis
>
>
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Re: [galaxy-dev] Advice on Galaxy administration

[Raymond Wan]

Hi Peter,

Thank you for the prompt reply and the clear answer!

Indeed, I don't want to ask for more than what I need (i.e., sudo)
since that would scare a lot of people.  However, I'd like to strike a
balance and be able to help users without pestering the system
administrators too much.

With administrator rights to just the Galaxy interface, I felt like my
hands were tied in terms of resolving some of the issues I was seeing
with the bwa toolbox.  It seems I was right.

I will see what could be done in terms of gaining command-line access
to the Galaxy directory.  Thank you for your advice!

Ray



On Wed, Sep 23, 2015 at 12:12 AM, Peter Cock  wrote:
> On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan  wrote:
>> Hi Peter,
>>
>>
>> On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock  
>> wrote:
>>> Hi Ray,
>>>
>>> You will absolutely need command line access to the Galaxy
>>> server for some of the administration tasks - the web admin
>>> controls and web report tool only let you do some of the likely
>>> tasks.
>>>
>>> During the initial setup admin (sudo) rights would be useful,
>>> at very least you'll need the sys admin to help with mounting
>>> shared network drives, cluster integration, database setup.
>>> If you want to run cluster jobs as the associated Unix account
>>> of each user, or anything like LDAP logins, then again you
>>> will need help from your sys admin.
>>
>>
>> I see!
>>
>> Sorry to go off on a tangent, but something I'm marginally familiar
>> with is content management systems (CMS) such as Joomla and WordPress
>> and maybe I can use it as an analogy to make sure I understand.  For
>> those, suppose we create an account "ray" who owns or is in a group
>> with the Apache process who owns:
>>
>> 1)  the directory that Joomla resides in and all subdirectories,
>> 2)  is the database administrator of the MySQL database, and
>> 3)  is the administrator of the Joomla web interface
>>
>> then I wouldn't need sudo access.  On occasion, the Apache
>> configuration might need to be changed and the system administrator
>> can be asked to do that, but that's probably once a year or something.
>>
>> Is Galaxy like this?  Or do you reckon I need full sudo access?
>>
>> Sorry, I just want to make sure when I ask for greater access, I have
>> an idea how Galaxy works or how it might differ from a CMS.
>>
>
> There are certainly similarities with the CMS idea - Galaxy
> also has its own user accounts, and interacts with Apache.
>
> I would certainly opt for a galaxy Linux user account with
> minimal rights (no sudo!), which would own all the files by
> default, and also galaxy specific database accounts (probably
> PostgreSQL not MySQL).
>
> We then install various Galaxy specific dependencies like
> samtools under $HOME/bin which is on the Galaxy user's
> $PATH - which like the main Tool Shed dependency mechanism
> installs tools locally without needing sys admin rights on the
> Galaxy server or cluster.
>
> When I have needed sudo has been during Galaxy setup
> (often), but only occasionally since (e.g. debugging and
> needing to restart services, or changing Apache settings).
>
> Peter
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Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP configuration

[David Trudgian]

Hi Carlos,

We aren’t using Active Directory here – but we do use an OpenLDAP directory 
which our cluster authenticates against, as does Galaxy. In order to track 
cluster usage for users running Galaxy jobs we use galaxy-pulsar between Galaxy 
itself and our SLURM cluster. Pulsar is configured to submit all jobs as a real 
user on the cluster, via SLURM-DRMAA. This means that all of the Galaxy usage 
on the cluster appears in our SLURM accounting database just like any other job 
would.  The complexity here is file ownership. Pulsar has to copy all input 
files into a staging directory, and change ownership to the real user for the 
job to run on the cluster. It is/was(?) a little complex to setup, as there are 
more parts involved then a typical Galaxy install, but it works great for us 
here.

When I was getting this setup John Chilton mentioned adding a PulsarEmbedded 
runner into Galaxy at some point. Not sure whether this has/is happening, but 
it’d make these situations easier:

https://trello.com/c/4YwVZBtq/1865-embedded-pulsar-job-runner


DT

--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833

From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Nicola Soranzo
Sent: Tuesday, September 22, 2015 5:59 AM
To: Carlos Lijeron ; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP 
configuration

Hi Carlos,
we are using Active Directory LDAP for user authentication, which works pretty 
well, but only the Galaxy user to submit jobs to the LSF cluster queue, so I 
can't help with the resource tracking.

Cheers,
Nicola
On 21/09/15 20:19, Carlos Lijeron wrote:
Everyone,

We are setting up Galaxy to work with our cluster and SLURM as the work 
manager.   The cluster itself authenticates to our local Active Directory, so 
I’m wondering if the best way to track resource utilization of Galaxy users on 
the cluster is to also have Galaxy authenticate to the same Active Directory 
LDAP.

Is anyone on this list using the same configuration and tracking resource 
utilization from Galaxy users submitting jobs to the cluster nodes?   Please 
advise.

Thank you all !


Carlos.




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[galaxy-dev] Current directory in the galaxy job file script

[Ping Luo]

I installed the latest Galaxy (v15.07) and tested with a job. I found my
local environment setup file was not executed. The line of code that
executes the local setup file is

[ -f "config/local_env.sh" ] && . config/local_env.sh

Further looking into the galaxy_xx.sh file shows the current directory of
the script is $working_directory before "cd $working_directory" is
executed. This is not the case in previous versions, where the job's
current directory is the root of the Galaxy server in the beginning, until
"cd $working_directory" is executed.

I think making the current directory first at the root of the Galaxy server
is better since I don't need to put a full path in galaxy.ini for the
environment_setup_file. Will you change this back to it was?


Thanks,

Ping
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Re: [galaxy-dev] Advice on Galaxy administration

[Peter Cock]

Hi Ray,

You will absolutely need command line access to the Galaxy
server for some of the administration tasks - the web admin
controls and web report tool only let you do some of the likely
tasks.

During the initial setup admin (sudo) rights would be useful,
at very least you'll need the sys admin to help with mounting
shared network drives, cluster integration, database setup.
If you want to run cluster jobs as the associated Unix account
of each user, or anything like LDAP logins, then again you
will need help from your sys admin.

See also: https://wiki.galaxyproject.org/Community/GalaxyAdmins

Peter


On Tue, Sep 22, 2015 at 9:07 AM, Raymond Wan  wrote:

> Dear all,
>
> I'm still new to Galaxy but was wondering if someone could offer some
> advice.
>
> On a local Galaxy instance, if I were the Galaxy administrator but do
> not have sudo access on the machine itself, is this a problem?  Or are
> the two roles intricately linked so that the Galaxy administrator will
> have to pester the system administrator frequently?  The web interface
> alone is not sufficient for the Galaxy administrator.
>
> (i.e., does a Galaxy administrator need sudo access ... or even just
> group access to the Galaxy subdirectory to effectively do his/her job?
>  ...I mean making Galaxy owned by a Unix group and putting the Galaxy
> administrator in that group.)
>
> As an aside, I was trying to do some alignment with bwa and realized I
> needed to prepare the genome by creating the index and an accompanying
> .loc file.  The instructions [1] seem to imply some kind of
> command-line access..
>
> Thank you for your help!
>
> Ray
>
> [1]  https://wiki.galaxyproject.org/Admin/DataPreparation
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Re: [galaxy-dev] parse history file/uploaded file with dynamic_options script

[Von Kuster, Greg]

Hi Linda,

I think your parameter definition will need to send the file_name of the 
HistoryDatasetAssociation, something like this...


> 
> 
> 
> 
> In my dynamic_options.py script, I want to parse the headers from 
> 'amplitudes' file and show them in the checkboxes section.
> 
> My problem seems to be the following.
> 
> In python, amplitudes is a galaxy object:
> 
> 
> How do I parse/access this file to get the headers?
> 
> It seems to be partly the same problem as asked last week in this 
> conversation:
> http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html
>  
> 
> Thanks!
> Linda
> 
> -- 
> Linda Bakker
> Bioinformatics Research Assistant
> Plant Research International, Wageningen UR
> Building 107 (Radix), room W1.Fa.054
> Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
> tel: +31-317-480756
> email: linda.bak...@wur.nl
> 
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Re: [galaxy-dev] parse history file/uploaded file with dynamic_options script

[Linda Bakker]

Hi Greg,
Wow that was easy!
I was not expecting that.
Thank you!
Linda


On 09/22/2015 03:41 PM, Von Kuster, Greg wrote:

Hi Linda,

I think your parameter definition will need to send the file_name of the 
HistoryDatasetAssociation, something like this...






In my dynamic_options.py script, I want to parse the headers from 'amplitudes' 
file and show them in the checkboxes section.

My problem seems to be the following.

In python, amplitudes is a galaxy object:


How do I parse/access this file to get the headers?

It seems to be partly the same problem as asked last week in this conversation:
http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html

Thanks!
Linda

--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl

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--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl

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[galaxy-dev] pbs_python can't be installed via scramble

[Makis Ladoukakis]

Hello everyone,

I'm trying to set up a Galaxy instance on a multi-core server in my university 
so according to the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of 
pbs_python

and tried to setup pbs_python via scramble:

LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

When I did that I got the error:

Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via 
PBS_PYTHON_INCLUDEDIR variable)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in 
egg.scramble()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble
self.run_scramble_script()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in 
run_scramble_script
raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( 
sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed 
for pbs_python 4.4.0

so I did some digging around and found that the file I need is in 

/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/

(please correct me if I am wrong)

So I tried again using:

 
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
 LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

but then I got the error:

In file included from src/C++/pbs_ifl.h:90:0,
 from src/C++/pbs_wrap.cxx:2978:
/usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No 
such file or directory
 #include "container.hpp"


Can someone help me please?

Kind regards,
Makis

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Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP configuration

[Nicola Soranzo]

Hi Carlos,
we are using Active Directory LDAP for user authentication, which works 
pretty well, but only the Galaxy user to submit jobs to the LSF cluster 
queue, so I can't help with the resource tracking.


Cheers,
Nicola

On 21/09/15 20:19, Carlos Lijeron wrote:

Everyone,

We are setting up Galaxy to work with our cluster and SLURM as the 
work manager.   The cluster itself authenticates to our local Active 
Directory, so I’m wondering if the best way to track resource 
utilization of Galaxy users on the cluster is to also have Galaxy 
authenticate to the same Active Directory LDAP.


Is anyone on this list using the same configuration and tracking 
resource utilization from Galaxy users submitting jobs to the cluster 
nodes?   Please advise.


Thank you all !


Carlos.


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[galaxy-dev] parse history file/uploaded file with dynamic_options script

[Linda Bakker]

Hi All,

I am a bit lost here.

In my xml I have the following sections:


label="amplitude file"/>
display="checkboxes" multiple="true" label="Mark quality control 
samples" dynamic_options='get_column_names(amplitudes)'/>





In my dynamic_options.py script, I want to parse the headers from 
'amplitudes' file and show them in the checkboxes section.


My problem seems to be the following.

In python, amplitudes is a galaxy object:


How do I parse/access this file to get the headers?

It seems to be partly the same problem as asked last week in this 
conversation:
http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html 



Thanks!
Linda

--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl

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Re: [galaxy-dev] Advice on Galaxy administration

[Raymond Wan]

Hi Peter,


On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock  wrote:
> Hi Ray,
>
> You will absolutely need command line access to the Galaxy
> server for some of the administration tasks - the web admin
> controls and web report tool only let you do some of the likely
> tasks.
>
> During the initial setup admin (sudo) rights would be useful,
> at very least you'll need the sys admin to help with mounting
> shared network drives, cluster integration, database setup.
> If you want to run cluster jobs as the associated Unix account
> of each user, or anything like LDAP logins, then again you
> will need help from your sys admin.


I see!

Sorry to go off on a tangent, but something I'm marginally familiar
with is content management systems (CMS) such as Joomla and WordPress
and maybe I can use it as an analogy to make sure I understand.  For
those, suppose we create an account "ray" who owns or is in a group
with the Apache process who owns:

1)  the directory that Joomla resides in and all subdirectories,
2)  is the database administrator of the MySQL database, and
3)  is the administrator of the Joomla web interface

then I wouldn't need sudo access.  On occasion, the Apache
configuration might need to be changed and the system administrator
can be asked to do that, but that's probably once a year or something.

Is Galaxy like this?  Or do you reckon I need full sudo access?

Sorry, I just want to make sure when I ask for greater access, I have
an idea how Galaxy works or how it might differ from a CMS.


> See also: https://wiki.galaxyproject.org/Community/GalaxyAdmins


Thanks for the link!  I'll take a look at it to get myself better
acquainted with administering Galaxy!

Ray
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