Re: [galaxy-dev] Using a Galaxy image on a local system

[Clare Sloggett]

Hi Alex & Enis,

Thanks very much!

I've only recently got VMware installed and am having a look at the NBIC VM
now. This is just the sort of thing I was looking for for quick start-up.

I've heard of the afgane project - it has been suggested to us that this
would be a good path to take for our local cloud. Is it specifically
designed for creating AMIs, or is it really for automated configuration and
deployment anywhere?

Thanks,
Clare

On Fri, Apr 29, 2011 at 8:48 AM, Enis Afgan  wrote:

> Hi Clare,
> Once you have a VM setup and accessible via ssh, you can also use our
> scripts for automated configuration and deployment of dependencies and
> tools. These scripts are used to setup Galaxy Cloud and they're targeted for
> Ubuntu 10.04 but should be applicable to other distributions as well. The
> scripts are available here:
> https://bitbucket.org/afgane/mi-deployment/overview
>
> Good luck,
> Enis
>
> On Thu, Apr 28, 2011 at 3:16 AM, Clare Sloggett wrote:
>
>> Hi all,
>>
>> I would like to set up Galaxy locally. At the moment, I'm just trying to
>> use it on my desktop (a Mac, OSX 10.6.7), but later we will want a local
>> server to play with.
>>
>> Rather than install galaxy and then install all the tools it can use (and
>> deal with OSX issues for some of them), it seems simpler just to use a
>> virtual machine, since there are images which get regularly updated and come
>> with pretty much everything. Is there anything wrong with this approach?
>>
>> I know there are Amazon EC2 images for Galaxy. So far as I know there are
>> not other kinds of images? So for using it on my desktop, I think my options
>> are either to run an EC2-compatible system locally, or to try to convert the
>> AMI to a VMWare or VirtualBox image. I was just wondering if anyone has
>> already tried either of these approaches?
>>
>> Also, is it possible to get hold of the galaxy AMI files themselves?
>>
>> Any advice welcome!
>>
>> Thanks,
>> Clare
>>
>>
>>
>> ___
>> 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/
>>
>
>
___
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/

[galaxy-dev] Restoring galaxy database return few empty tables.

[Vipin TS]

Dear Galaxy Team,

I am switching our Galaxy production service to a new machine, We are using
Postgres as database server.
The existing database belongs to postgres version 8.3 and I took my
instance's dump using postgres version 8.4.
I am able to restore my database on postgres 8.4, Except few tables were
empty and with few strange
error message left on log file. I am not sure how many tables are empty, but
I found table called 'job' returns 0 rows.
Original job table returns me 40733 rows.

excerpts from error log:
ERROR:  insert or update on table
"history_dataset_association_annotation_association" violates foreign key
constraint "history_dataset_association_a_history_dataset_association__fkey"
DETAIL:  Key (history_dataset_association_id)=(284985) is not present in
table "history_dataset_association".
STATEMENT:  ALTER TABLE ONLY
history_dataset_association_annotation_association
ADD CONSTRAINT
history_dataset_association_a_history_dataset_association__fkey FOREIGN KEY
(history_dataset_association_id) REFERENCES history_dataset_association(id);
ERROR:  insert or update on table
"history_dataset_association_tag_association" violates foreign key
constraint "history_dataset_association_t_history_dataset_association__fkey"
DETAIL:  Key (history_dataset_association_id)=(387932) is not present in
table "history_dataset_association".
STATEMENT:  ALTER TABLE ONLY history_dataset_association_tag_association

In my knowledge we didn't do any manual transactions on Galaxy database and
Could anyone let me know something
wrong at my end. I'm sure this has been covered somewhere but I haven't been
able to find it on the Wiki or by searching the archives.

Thanks in advance, Vipin
Friedrich Miescher Laboratory
of the Max Planck Society
Spemannstrasse 39, 72076
Tuebingen, Germany
___
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/

Re: [galaxy-dev] python2.6?

[Nate Coraor]

Yamshchikov, Vladimir wrote:
> Hello all,
> 
> If this question is not for this list, please advise. Both my RHEL55 and SL55 
> are based on python 2.4.3  - how I can add python 2.6 support for Galaxy 
> without screwing up OS? I had both 2.4 and 2.6 installed, by python -V 
> returns only 2.4.3.  When I uninstalled 2.4.3, SL55 self-destructed, the same 
> will happen with RHEL55. I was advised that 2.6 should not ever be made seen 
> (like manipulating $PATH)  by the system that depends on 2.4 - so how I add 
> 2.6 if it is needed for full functionality?

Hi Vladimir,

You could install 'python26' from EPEL[1], presumably this does not
break /usr/bin/python since it installs the new version as
/usr/bin/python2.6.  Then as the user which runs Galaxy, do something
like this:

$ mkdir $HOME/bin
$ ln -s /usr/bin/python2.6 $HOME/bin/python
$ export PATH=$HOME/bin:$PATH
$ echo 'export PATH=$HOME/bin:$PATH' >> $HOME/.bash_profile

--nate

[1] http://fedoraproject.org/wiki/EPEL

> 
> 

> ___
> 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/

___
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/

[galaxy-dev] python2.6?

[Yamshchikov, Vladimir]

Hello all,

If this question is not for this list, please advise. Both my RHEL55 and SL55 
are based on python 2.4.3  - how I can add python 2.6 support for Galaxy 
without screwing up OS? I had both 2.4 and 2.6 installed, by python -V returns 
only 2.4.3.  When I uninstalled 2.4.3, SL55 self-destructed, the same will 
happen with RHEL55. I was advised that 2.6 should not ever be made seen (like 
manipulating $PATH)  by the system that depends on 2.4 - so how I add 2.6 if it 
is needed for full functionality?


___
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/

Re: [galaxy-dev] connecting to a DB on a different host

[Nate Coraor]

Nikolai Vazov wrote:
> 
> Hi, Nate,
> 
> I followed your instructions and managed to compile the psycopg2.
> 
> What I did:
> 
> 1. Downloaded a tar.gz of psycopg2 2.0.13 to
> /home/galaxy/galaxy-dist and unpacked it there
> 2. cd into psycopg2, modified the setup.py according to your
> instructions (added the line containing scramble_lib)
> 3. added the file ez_setup.py to
> /home/galaxy/galaxy-dist/scripts/scramble/lib/, the same dir where
> scramble_lib.py is located
> 4. ran PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib
> python26 setup.py egg_info --tag-build=_8.4.2_static bdist_egg
> 
> the output is attached (looks ok)
> 
> 5. ran run.sh (database_connection =
> postgres://user:pass@host:5432/vd_galaxy?sslmode=require) and got
> the error
> 
> OperationalError: (OperationalError) sslmode value "require" invalid
> when SSL support is not compiled in
> 
> Was the new egg version taken into account?

Whoops, missed a step!  Copy:

  
/home/galaxy/galaxy-dist/psycopg2-2.0.13/dist/psycopg2-2.0.13_8.4.2_static-.egg
 

to:

  /home/galaxy/galaxy-dist/eggs

--nate

> 
> Nikolay
> 
> -- 
> Nikolay Vazov, PhD
> Research Computing Centre - http://hpc.uio.no
> USIT, University of Oslo


___
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/

Re: [galaxy-dev] connecting to a DB on a different host

[Nikolai Vazov]

Hi, Nate,

I followed your instructions and managed to compile the psycopg2.

What I did:

1. Downloaded a tar.gz of psycopg2 2.0.13 to /home/galaxy/galaxy-dist 
and unpacked it there
2. cd into psycopg2, modified the setup.py according to your 
instructions (added the line containing scramble_lib)
3. added the file ez_setup.py to 
/home/galaxy/galaxy-dist/scripts/scramble/lib/, the same dir where 
scramble_lib.py is located
4. ran PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib 
python26 setup.py egg_info --tag-build=_8.4.2_static bdist_egg


the output is attached (looks ok)

5. ran run.sh (database_connection = 
postgres://user:pass@host:5432/vd_galaxy?sslmode=require) and got the 
error


OperationalError: (OperationalError) sslmode value "require" invalid 
when SSL support is not compiled in


Was the new egg version taken into account?

Nikolay

--
Nikolay Vazov, PhD
Research Computing Centre - http://hpc.uio.no
USIT, University of Oslo

output_egg_compilation_psycopg2
Description: Binary data
___
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/

Re: [galaxy-dev] Display BAM with IGV

[Dave Walton]

Could someone who has successfully gotten the IGV tool to work using NGINX as 
your proxy, tell me if there was anything specific they needed to do with their 
NGINX or galaxy config to get it working?

Thanks,

Dave


On 4/27/11 9:07 PM, "Dave Walton"  wrote:

I’m getting this same error and I’m running nginx as a proxy server.  Is there 
a specfic parameter we should be aware of to allow partial gets?  I don’t see 
anything in the wiki page for setting up the ProductionServer.

Thanks,

Dave


On 4/27/11 12:33 PM, "Daniel Blankenberg"  wrote:

Hi Alex,

Displaying BAM files at external applications usually requires an http server 
that supports partial gets. Unfortunately, the current lightweight http server 
that is built into Galaxy does not support these advanced http options.  
However, this limitation can be overcome by using a proxy server that is able 
to handle http1.1 requests. Please see "Using a Proxy server" at 
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for 
help on setting this up.

Thanks for using Galaxy,

Dan


On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote:

Hello all,
I just updated our local copy of Galaxy and just wanted to try the new IGV 
display application.
When I try to display a BAM file with the local IGV or the web IGV I encounter 
following error complaining about the Null content-length.
Has any of you encountered the same problem? Do I miss something?
Thanks in advance

Alex


INFO [2011-04-27 16:00:14,440]  [TrackManager.java:225] [Thread-6]  Loading1 
resources.
ERROR [2011-04-27 16:00:14,589]  [SeekableHTTPStream.java:59] [Thread-6]  Null 
content-length for: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
ERROR [2011-04-27 16:00:14,590]  [TrackLoader.java:821] [Thread-6]  Error 
loading sam track
java.lang.RuntimeException: Error loading file: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length
at org.broad.igv.util.SeekableHTTPStream.(SeekableHTTPStream.java:60)
at 
org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80)
at 
org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97)
at 
org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75)
at 
org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.java:69)
at 
org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54)
at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761)
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282)
at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148)
at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88)
at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193)
at org.broad.igv.main.CommandListener.run(CommandListener.java:93)
at java.lang.Thread.run(Thread.java:636)
ERROR [2011-04-27 16:00:14,592]  [TrackLoader.java:211] [Thread-6]  
java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length



___

  Alexander Graf

Laboratory of Functional Genome Analysis
Gene Center, University of Munich (LMU)
Feodor-Lynen-Strasse 25; 81377 Munich; Germany
email: g...@lmb.uni-muenchen.de
Internet: www.lafuga.de/genomics.htm 
 ___

___
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/



___
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/

[galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output

[Peter Cock]

Hi all,

I mentioned just over a month ago that I had written a Galaxy tool
to do find Reciprocal Best Hits (RBH) from BLAST tabular output
or similar (e.g. Bill Pearson's FASTA tabular output).

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html

The only problem I had was setting default columns, which I
consider to be a minor bug in Galaxy:

https://bitbucket.org/galaxy/galaxy-central/issue/507

Regardless of this small usability issue, would the Galaxy team
like to add this tool to the main distribution (to sit along with my
BLAST+ wrappers), or should I submit it to the tool shed?

If you want to merge it, the following change set should suffice:
https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30

I made a subsequent change set to test giving column defaults
as value="c2" rather than value="c2" which makes no difference,
but if this is how default column values are meant to be given,
take this change too:
https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30

Thanks,

Peter
___
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/

[galaxy-dev] Problem with Torque/Maui

[Marco Moretto]

Hi all,
first of all, thanks to the Galaxy Team for this really useful software.
Actually I don't really know if my problem is related with Galaxy or with
Torque/Maui but I didn't find any solution looking in both Torque and Maui
user lists, so I hope that some of you with more experience could give me
some good advices. I'm trying to set up Galaxy in a small local virtual
environment in order to test it. I started with 2 virtual ubuntu servers
called galaxy1 and galaxy2. On galaxy1 I succesfully installed Galaxy,
Apache, Torque and Maui. I'm using Postgres ad DBMS. It is installed on
another "real" DB server. The virtual server galaxy2 is used as node. Galaxy
is working like a charm locally but when I try to use Torque problems arise.
Torque alone works correctly. That means that I can submit a job with qsub
and everything works. The 2 virtual server (galaxy1 and galaxy2) share a
directory (through NFS) in which I installed Galaxy following the "unified
method" from the documentation.
Now, as I said, Galaxy alone works, Torque/Maui alone works. When I put the
two together nothing works.
As a test I upload (using local runner) a gff file. Then I try to make a
filter to the gff using "Filter and sort -> Extract features". When I run
this tool the corresponding job on the Torque queue runs forever in Hold
state. I report some output from diagnose programs:
The diagnose -j reports the following:

Name  State Par Proc QOS WCLimit R  Min User
 Group  Account  QueuedTime  Network  Opsys   ArchMem   Disk  Procs
  Class Features

29 Hold DEF1 DEF 1:00:00 01   galaxy
galaxy-00:02:36   [NONE] [NONE] [NONE]>=0>=0NC0
[batch:1] [NONE]

While the showq command reports

ACTIVE JOBS
JOBNAMEUSERNAME  STATE  PROC   REMAINING
 STARTTIME


 0 Active Jobs   0 of1 Processors Active (0.00%)

IDLE JOBS--
JOBNAMEUSERNAME  STATE  PROC WCLIMIT
 QUEUETIME


0 Idle Jobs

BLOCKED JOBS
JOBNAMEUSERNAME  STATE  PROC WCLIMIT
 QUEUETIME

29   galaxy   Hold 1 1:00:00  Wed May  4
03:56:40


The checkjob reports:
checking job 29

State: Hold
Creds:  user:galaxy  group:galaxy  class:batch  qos:DEFAULT
WallTime: 00:00:00 of 1:00:00
SubmitTime: Wed May  4 03:56:40
  (Time Queued  Total: 00:03:07  Eligible: 00:00:01)

The qstat -f reports

Job Id: 33.galaxy1.research.intra.ismaa.it
Job_Name = 27_extract_features1_marco.more...@iasma.it
Job_Owner = gal...@galaxy1.research.intra.ismaa.it
job_state = W
queue = batch
server = galaxy1.research.intra.ismaa.it
ctime = Wed May  4 04:56:36 2011
Error_Path =
galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.e

exec_host = galaxy2/0
exec_port = 15003
Execution_Time = Wed May  4 05:26:41 2011
mtime = Wed May  4 04:56:37 2011
Output_Path =
galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.
o
qtime = Wed May  4 04:56:36 2011
Resource_List.neednodes = 1
Resource_List.nodect = 1
Resource_List.nodes = 1
Resource_List.walltime = 01:00:00
stagein = /mnt/equallogic1/galaxy/tmp/dataset_18.dat@galaxy1
:/mnt/equallog
ic1/galaxy/galaxy-dist/database/files/000/dataset_18.dat,
/mnt/equallogic1/galaxy/tmp/dataset_30.dat@galaxy1
:/mnt/equallogic1/g
alaxy/galaxy-dist/database/files/000/dataset_30.dat
stageout =
/mnt/equallogic1/galaxy/galaxy-dist/database/files/000/dataset_
30.dat@galaxy1
:/mnt/equallogic1/galaxy/galaxy-dist/database/files/000/
dataset_30.dat
substate = 37
Variable_List = PBS_O_QUEUE=batch,
PBS_O_HOST=galaxy1.research.intra.ismaa.it
euser = galaxy
egroup = galaxy
hashname = 33.galaxy1.research.intra.ismaa.it
queue_rank = 33
queue_type = E

StartDate: -00:03:06  Wed May  4 03:56:41
Total Tasks: 1

Req[0]  TaskCount: 1  Partition: DEFAULT
Network: [NONE]  Memory >= 0  Disk >= 0  Swap >= 0
Opsys: [NONE]  Arch: [NONE]  Features: [NONE]


IWD: [NONE]  Executable:  [NONE]
Bypass: 0  StartCount: 1
PartitionMask: [ALL]
PE:  1.00  StartPriority:  1
cannot select job 29 for partition DEFAULT (non-idle state 'Hold')

and finally the tracejob reports

/var/spool/torque/server_priv/accounting/20110504: Permission denied
/var/spool/torque/mom_logs/20110504: No such file or directory
/var/spool/torque/sched_logs/20110504: No such file or directory

Job: 33.galaxy1.research.intra.ismaa.it

05/04/2011 04:56:36  Senqueuing into batch, state 1 hop 1
05/04/2011 04:56:36  SJob Queued at request of
gal...@galaxy1.research.intra.ismaa.it, owner =
gal...@galaxy1.research.intra.ismaa.it, job name =
  27_extract_features1_marco.more...@iasma.it, queue
= batch
05/04/2011 04:56:37  SJob Run at request of
gal