Re: [galaxy-dev] help with users and postgres

[Hans-Rudolf Hotz]

On 01/25/2011 03:44 PM, Davide Cittaro wrote:


On Jan 25, 2011, at 3:40 PM, Hans-Rudolf Hotz wrote:


Hi Davide

We were in a similar situation when we switched to external authentication. 
Although, only one user was affected and we were using MySQL.

I could fix it by changing the contents of the galaxy_user with a few sql 
statements. BUT, be careful! you can do a lot of damage to the database.



Could you post the sql statement? I guess that should work in the same way!
Thanks
d


Have a look at the galaxy_user table to identify the 'broken' row, ie 
the wrong e-mail.



and then you can execute:

   update galaxy_user set email = f...@fmi.ch where email =
   wrong_name@wrong_host.ch;



you might have to change the name in the role table accordingly.


Once again be careful with what you are doing, and don't blame me if you 
create a mess   ;)




Hans


Regards, Hans




On 01/25/2011 02:40 PM, Davide Cittaro wrote:

Dear all,
Our local galaxy instance uses apache authentication to log users. This said, some users have no 
User Name and some other have a wrong User name (probably because they have 
been added before the apache integration). I just wonder if there's a way to modify the user names 
directly in the postgres database (I'm pretty sure that is possible...).

Thanks

d
/*
Davide Cittaro, PhD

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.citt...@ifom-ieo-campus.it
*/








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/*
Davide Cittaro, PhD

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.citt...@ifom-ieo-campus.it
*/






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Re: [galaxy-dev] listing the same tool twice in tool_conf.xml

[Hans-Rudolf Hotz]

On 02/21/2011 04:05 PM, Branden Timm wrote:

Hi All,
My group is trying to create some custom sections in the Tools pane, and
have run into an issue. We have a custom section, within which there are
three different labels and several tools under each label. We are trying
list the same tool under two different labels within the same section.
However, the second occurrence of the tool is not displayed. Is it
possible to list the same tool twice under the same section?



Hi Brandon

make a copy of the tool definition xml file and change the value for 
'id' in the first line and then refer to the copy in the tool_conf.xml 
file for the second occurrence .that should do the trick.



Regards, Hans





Branden Timm
bt...@glbrc.wisc.edu
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Re: [galaxy-dev] Local Galaxy implimentation

[Hans-Rudolf Hotz]

Hi Lee



*   What is a realistic amount of someones time to implement Galaxy on a Linux  
server so that it can be used by researchers using the Web?


Galaxy is simple to set up and works out-of-the-box. You will have a 
functional Galaxy server within minutes (yes, 'within minutes').



Providing Galaxy in a production environment will need a few extra steps 
(see: 
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer 
). Depending on your needs, not all the steps are required. I highly 
recommend, that you use PostgreSQL or MySQL (instead of the built in 
SQLite) from day 1. Nevertheless, you should have a reliable server 
within a few days.




*   What is the usual time overhead to keep it running and how skilled would 
they have to be?


Galaxy itself needs hardly any maintenance. However, it is advised to 
update the code on a regularly basis. Currently we do it every three 
months. We have a test and a production server, so the update process is 
split over two days, with a couple of days testing in between. The 
actual code updates have been very smooth so far and require about an 
hour of downtime.


As long as you have support from your IT-Department running the 
hardware, you don't need extraordinary skills. Galaxy is written in 
Python, but you don't need to be a Python programmer (even if you want 
to make a few changes), as long as you have some basic programming 
skills in another language.


There is a lot of information on the wiki (sometimes, the info is 
difficult to find). And if you get stuck, you can always send an e-mail 
to galaxy-dev


Of course, it all changes when you add your own tools. Although, the 
actual addition is simple. You might need some extra time for testing 
and improving your tools. Also, don't forget the time required to teach 
the use of Galaxy in general and the use of the self-written tools to 
your colleagues at the bench.


Regards, Hans




Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland




I should say, this will be for local biological researchers only, approx 20-30 
dealing in Exome and Whole genome sequences.

Best regards
Lee

--
Dr Lee Hazelwood
BHRC Bioinformatics Technology Group Leader
Biomedical and Health Research Centre
Faculty of Biological Sciences
Garstang Building,
University of Leeds,
Leeds,
LS2 9JT, UK.
E-mail: l.d.hazelw...@leeds.ac.ukmailto:l.d.hazelw...@leeds.ac.uk




Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org




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Re: [galaxy-dev] Recommended Specs for Production System

[Hans-Rudolf Hotz]

On 04/07/2011 11:40 PM, Ryan Golhar wrote:

Hi all - So, I been asked to provide specs for a production Galaxy
system to support approximately 20-30 users. Most of these users are new
to bioinformatics and very new to NGS. I'm targeting a user base that
will use a light to moderate amount of NGS data.

I've looked at the the Produce Server Wiki page stuff, but I'm curious
what everyone else is using or recommends? How big of a compute cluster,
how much storage, proxy/web server configurations, etc, etc.

If you had to deploy a production system, based on what you know, what
would you choose?



Hi Ryan


I would go for a single (multicore) box. With just 20-30 users who are 
'new to bioinformatics' you will hardly ever have more than 3 users 
using Galaxy at the same time - you can always limit the number of 
concurrent galaxy jobs in the universe_wsgi.ini file 
('local_job_queue_workers').


Since you are expecting NGS data, having the right amount of RAM would 
be my biggest concern. What do you mean by light to moderate amount of 
NGS data? are you talking about the number of samples to process or are 
you talking about the individual size of the sample. The latter will 
have an impact on the required amount of RAM. On the other hand both 
will have an impact on the amount of storage required.


You have to make the calculations for required storage and RAM first, 
but this is independent of whether you use Galaxy or not. The only risk 
when offering NGS tools via galaxy it might be to easy to run them 
resulting in a lot of 'garbage' or redundant NGS processing. That's why 
it is important to disable anonymous access so you can track who is 
doing what.


Using external authentication is very handy. However, it does restrict 
you to users already in you 'network'. We are using it, and it is 
sometimes annoying, as I can't have temporary guest accounts - our IT 
guys would have to create a new 'member' of our institute for every 
guest



Hope this helps, Hans



Ryan



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Re: [galaxy-dev] Fwd: configuration of reports at galaxy

[Hans-Rudolf Hotz]

On 04/12/2011 09:20 AM, hari krishna wrote:

Hi,
Thanks for your immediate reply,
ya same thing i tried but i cant able to open that page.. giving
error as  cant able to locate http://your host:different port number/
address   is coming .
 my be i did wrong at configuration , can you give proper link for
that.



always do a 'reply all' so everybody can benefit from any 
comments/questions



do you mean the link to the wiki?

https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_06_08




Hans



On Tue, Apr 12, 2011 at 12:35 PM, Hans-Rudolf Hotzh...@fmi.ch  wrote:


Hi

are you looking at the right page? The reports are not part of the admin
view. You have to go to a different URL which probably looks like:


http://your host:different port number/

see the June 8, 2010 New Development News Brief for a quick explanation



Regards, Hans




On 04/12/2011 08:32 AM, hari krishna wrote:



Hi,
  hi can any one explain how can i get reports per tool option in
galaxy,
  I tried by configurating reports_wsgi.ini by changing the different
port number.
  and started #sh ru_reports.sh

  As an galaxy administrator i didnt find the Jobs per tool option.

 can any one explain the configuration procedure for getting job per
tool option.





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Re: [galaxy-dev] Error when adding datasets

[Hans-Rudolf Hotz]

On 04/14/2011 07:36 PM, Greg Von Kuster wrote:

Hello Louise,

I've CC'd Nate on this as he may be able to help - although no guarantees.  I'm 
not expert enough in this area to know where to look for the cause.  Perhaps 
someone in the community can help as well.

It is likely that LDAP is playing a role in this behavior.




Hi

I am sure you have tested everything, but just to double check

 - is your PostgreSQL database in sync with the database folder?

 - are you sure there is no second galaxy installation accessing the
   same PostgreSQL database?

 - you mention, that you have started with an empty PostgreSQL
   database, so this last question does probably not apply: make sure
   you have the right user names (you even run into trouble with case
   sensitivity) in your PostgreSQL database. We had troubles when we
   switched to external authentication: some users just couldn't work
   anymore, ie could not create new history items anymore. The problem
   was then solved by fixing their user names in the (MySQL) database.


Regards, Hans





On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote:


The thing is, we use LDAP logging so we can't even access the website
without logging in.
Moreover, when I logged in, I arrived on the data analysis page where the
automatic unnamed history was obviously created in the history panel.

I forgot to mention we have issues creating and deleting histories, like,
we can't access some histories and everytime we delete histories, two extra
unnamed histories are created. As I mentioned before, it is also impossible
to load a dataset in any history, existing or not.

Do you think it could be linked to our using LDAP?

Thanks
L-A


On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kusterg...@bx.psu.edu
wrote:

On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote:


Here is the result I got from the debug statements:

galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
history: None


This is the problem - when you registered normally, a history would have
been automatically created for you.  But somehow you don't have a

history -

no idea why / how this happened, but it is very unlikely this is a

result

of a bug within Galaxy.  Try logging out and logging in again and a new
history should be created for you.



galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans:galaxy.web.framework.GalaxyWebUITransaction object at
0x29f40950
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans.sa_session:sqlalchemy.orm.scoping.ScopedSession object at
0x19ab21d0

Thanks again
L-A


Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit :

I assume when you dropped the old database and recreated the new,
empty database, you made sure the database connection string in
universe_wsgi.ini was correctly set.  if so, when you started up
Galaxy, it would have created all of the required tables in the new
database, and they would all be empty.  When you first registered as
the admin user, it would have automatically populated several tables
with data, including the history table.  One or more of these things
must not have been successful.


To attempt to narrow down the problem, I'll need you to do the
following.  Here are lines # 905 - 907 in
~/lib/galaxy/web/controllers/library-common.py


   # Send the current history to the form to enable importing
datasets from history to library
   history = trans.get_history()
   trans.sa_session.refresh( history )


Please add the following debug statements:


   # Send the current history to the form to enable importing
datasets from history to library
   history = trans.get_history()
   log.debug(### history: %s % str( history ))
   log.debug(### trans: %s % str( trans ))
   log.debug(### trans.sa_session: %s %
str( trans.sa_session ))
   trans.sa_session.refresh( history )


Stop and restart your Galaxy server after making the above changes,
and reply back with the output of the debug statements.  Assuming you
start your Galaxy instance with:


sh run.sh


you'll see the results of the debug statements in the log scrolling in
the window in which you started Galaxy.


Thanks


On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote:


Hello Greg

Thank you for answering. Please find the answers after each
question.


Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit :

Hello Louise,

I do not think this issue is related to the Galaxy eggs, but
instead looks like a data issue of some kind.  Please replly back
with answers to the following questions.

How did you create your database?


Couldn't have done it more simply ^^:
CREATE DATABASE galaxy_db;
GRANT ALL ON DATABASE galaxy_db TO galaxy;
executed in psql.
The very same way I did for the one that's still working fine.


Did you populate it with any data exported from another database?



In the beginning yes but when I saw that error I dropped the
database
and 

Re: [galaxy-dev] Error when adding datasets

[Hans-Rudolf Hotz]

On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote:

Hi Hans, thanks for your reply.



   - is your PostgreSQL database in sync with the database folder?


I'm sorry I'm not sure I get what you mean, what folder is it?



the folder where you keep the datasets, eg:

your local path/galaxy_dist/database/

and it particular

your local path/galaxy_dist/database/files/000/dataset_*.dat

if you have an empty PostgreSQL database, then there should also be no 
datasets.



Hans




   - are you sure there is no second galaxy installation accessing the
 same PostgreSQL database?


Never been this sure of something before. :) I installed both galaxy and
postgresql myself so I can guarantee there's ony one galaxy install on
it.



   - you mention, that you have started with an empty PostgreSQL
 database, so this last question does probably not apply: make sure
 you have the right user names (you even run into trouble with case
 sensitivity) in your PostgreSQL database. We had troubles when we
 switched to external authentication: some users just couldn't work
 anymore, ie could not create new history items anymore. The problem
 was then solved by fixing their user names in the (MySQL) database.


Yes, the username is properly created in the database when I log in on
an empty database. We never used anything besides LDAP anyway.



Regards, Hans


Cheers,
L-A







On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote:


The thing is, we use LDAP logging so we can't even access the website
without logging in.
Moreover, when I logged in, I arrived on the data analysis page where the
automatic unnamed history was obviously created in the history panel.

I forgot to mention we have issues creating and deleting histories, like,
we can't access some histories and everytime we delete histories, two extra
unnamed histories are created. As I mentioned before, it is also impossible
to load a dataset in any history, existing or not.

Do you think it could be linked to our using LDAP?

Thanks
L-A


On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kusterg...@bx.psu.edu
wrote:

On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote:


Here is the result I got from the debug statements:

galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
history: None


This is the problem - when you registered normally, a history would have
been automatically created for you.  But somehow you don't have a

history -

no idea why / how this happened, but it is very unlikely this is a

result

of a bug within Galaxy.  Try logging out and logging in again and a new
history should be created for you.



galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans:galaxy.web.framework.GalaxyWebUITransaction object at
0x29f40950
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans.sa_session:sqlalchemy.orm.scoping.ScopedSession object at
0x19ab21d0

Thanks again
L-A


Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit :

I assume when you dropped the old database and recreated the new,
empty database, you made sure the database connection string in
universe_wsgi.ini was correctly set.  if so, when you started up
Galaxy, it would have created all of the required tables in the new
database, and they would all be empty.  When you first registered as
the admin user, it would have automatically populated several tables
with data, including the history table.  One or more of these things
must not have been successful.


To attempt to narrow down the problem, I'll need you to do the
following.  Here are lines # 905 - 907 in
~/lib/galaxy/web/controllers/library-common.py


# Send the current history to the form to enable importing
datasets from history to library
history = trans.get_history()
trans.sa_session.refresh( history )


Please add the following debug statements:


# Send the current history to the form to enable importing
datasets from history to library
history = trans.get_history()
log.debug(### history: %s % str( history ))
log.debug(### trans: %s % str( trans ))
log.debug(### trans.sa_session: %s %
str( trans.sa_session ))
trans.sa_session.refresh( history )


Stop and restart your Galaxy server after making the above changes,
and reply back with the output of the debug statements.  Assuming you
start your Galaxy instance with:


sh run.sh


you'll see the results of the debug statements in the log scrolling in
the window in which you started Galaxy.


Thanks


On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote:


Hello Greg

Thank you for answering. Please find the answers after each
question.


Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit :

Hello Louise,

I do not think this issue is related to the Galaxy eggs, but
instead looks like a data issue of some kind.  Please replly back
with answers to the following questions.

How did you 

Re: [galaxy-dev] Error when adding datasets

[Hans-Rudolf Hotz]

On 04/18/2011 11:28 AM, Louise-Amélie Schmitt wrote:

Hello again

I tried deleting the compiled templates like Sarah Diehl did for her
user registration issue:


first thank you for your help. I tried reloading everything, cleared

the cache of my browser and tried it on a different computer whose
browser never before was on the Galaxy website. All of this did not
work. What worked in the end was deleting the compiled_templates
directory.

But it didn't work either. I'm back to square one, with no option in
sight. I keep getting the same error message when trying to add
datasets.

Any idea?


well, do it the hard way and start from square one:

- is galaxy working out of the box (fresh checkout, using SQLite)

- is galaxy working out of the box (using a non-root user called
  galaxy, using a fresh checkout downloaded and installed into the
  galaxy user home directory and use PostgreSQL)

   + is it still working when you change to require_login = True

   + is it still working when you change to use_remote_user = True


at which point does it stop working?



Hans




Cheers,
L-A


Le vendredi 15 avril 2011 à 16:52 +0200, Louise-Amélie Schmitt a écrit :

Ooops, this is very right, I totally forgot about that. It woud have
become problematic at some point I guess. Thank you for pointing this
out!

I changed it so the new database is associated with brand new
appropriate directories. (and dropped and re-created the db again) But I
keep getting the same error message with supposedly nonexistent
histories.

Thanks again
L-A

Le vendredi 15 avril 2011 à 13:47 +0200, Hans-Rudolf Hotz a écrit :


On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote:

Hi Hans, thanks for your reply.



- is your PostgreSQL database in sync with the database folder?


I'm sorry I'm not sure I get what you mean, what folder is it?



the folder where you keep the datasets, eg:

your local path/galaxy_dist/database/

and it particular

your local path/galaxy_dist/database/files/000/dataset_*.dat

if you have an empty PostgreSQL database, then there should also be no
datasets.


Hans




- are you sure there is no second galaxy installation accessing the
  same PostgreSQL database?


Never been this sure of something before. :) I installed both galaxy and
postgresql myself so I can guarantee there's ony one galaxy install on
it.



- you mention, that you have started with an empty PostgreSQL
  database, so this last question does probably not apply: make sure
  you have the right user names (you even run into trouble with case
  sensitivity) in your PostgreSQL database. We had troubles when we
  switched to external authentication: some users just couldn't work
  anymore, ie could not create new history items anymore. The problem
  was then solved by fixing their user names in the (MySQL) database.


Yes, the username is properly created in the database when I log in on
an empty database. We never used anything besides LDAP anyway.



Regards, Hans


Cheers,
L-A







On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote:


The thing is, we use LDAP logging so we can't even access the website
without logging in.
Moreover, when I logged in, I arrived on the data analysis page where the
automatic unnamed history was obviously created in the history panel.

I forgot to mention we have issues creating and deleting histories, like,
we can't access some histories and everytime we delete histories, two extra
unnamed histories are created. As I mentioned before, it is also impossible
to load a dataset in any history, existing or not.

Do you think it could be linked to our using LDAP?

Thanks
L-A


On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kusterg...@bx.psu.edu
wrote:

On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote:


Here is the result I got from the debug statements:

galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
history: None


This is the problem - when you registered normally, a history would have
been automatically created for you.  But somehow you don't have a

history -

no idea why / how this happened, but it is very unlikely this is a

result

of a bug within Galaxy.  Try logging out and logging in again and a new
history should be created for you.



galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans:galaxy.web.framework.GalaxyWebUITransaction object at
0x29f40950
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans.sa_session:sqlalchemy.orm.scoping.ScopedSession object at
0x19ab21d0

Thanks again
L-A


Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit :

I assume when you dropped the old database and recreated the new,
empty database, you made sure the database connection string in
universe_wsgi.ini was correctly set.  if so, when you started up
Galaxy, it would have created all of the required tables in the new
database, and they would all be empty.  When you first registered

Re: [galaxy-dev] substitute or replace a value?

[Hans-Rudolf Hotz]

Hi David

Have you looked into the excellent Galaxy Unix-Tools package created 
by Gordon Assaf?


http://hannonlab.cshl.edu/galaxy_unix_tools/index.html

The Find  Replace text in line/column tool is probably what you are 
looking for:


http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html#find_and_replace


regards, Hans



On 04/25/2011 11:20 PM, Jennifer Jackson wrote:

Hello David,

There are tools to select data based on defined attributes or to perform
calculations on existing data (Text Manipulation, Filter and Sort), but
as such no direct user-defined substitution tools.

Very sorry for any inconvenience,

Best,

Jen
Galaxy team

On 2/23/11 9:26 AM, David Hoover wrote:

Is there a tool for doing a global or column-based substitution in a
text or tabular file? For example, replace all instances of the number
2 in a column to a number 1?


David Hoover
Helix Systems Staff
http://helix.nih.gov


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Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

[Hans-Rudolf Hotz]

Hi Ed

You can use the variable $userEmail in the 'command' tag of the tool 
definition file


Regards, Hans



On 05/06/2011 03:56 AM, Edward Kirton wrote:

is there a variable i can use in the tool config xml file?
thanks!
ed




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Re: [galaxy-dev] Uploading Binary Files into Galaxy

[Hans-Rudolf Hotz]

Hi Darren

I assume, you have created a new data type

https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes


You can now disable the 'sniffing' by adding the data type to the 
following line:


unsniffable_binary_formats = [ 'ab1', 'scf' ]

in:

~/galaxy-dist/lib/galaxy/datatypes/binary.py



I hope this helps

Regards, Hans



On 05/06/2011 03:59 AM, darren.culle...@csiro.au wrote:

Hi Everyone,

I have encountered a problem and I don't know how to fix it.

We have built a Galaxy instance on a couple of machines here and have built the 
XML files to use a couple of tools in Galaxy. The input of one of these is a 
Suffix Array (a binary file). Unfortunately, when I try and upload the Suffix 
Array, I get the following error message:

The uploaded binary file contains inappropriate content

My gut feeling is that it is related to Galaxy trying to preview the file and 
not being able to determine the type. Is there any way around this? I can 
provide the file and the tool if you need to investigate it further.

Thanks,


Darren Cullerne
Computational Biology
CSIRO Plant Industry

x5042
+61 2 62465042

darren.culle...@csiro.aumailto:darren.culle...@csiro.au




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Re: [galaxy-dev] sqlite to postgres

[Hans-Rudolf Hotz]

Hi Harendra

I am not aware of anybody who made this kind of transition without 
running into all kind of problems. I suggest the following workaround:


- set up a new, independent Galaxy server using PostgreSQL.
- transfer the histories you want to keep to the new server using the
  'Export to File' option on the old server followed by the 'Import to
  File' option on the new server.


Regards, Hans


On 06/02/2011 12:01 PM, Harendra chawla wrote:

Hi,

I want to convert my database from sqlite to postgres. I am able to do it as
far as schema is concerned, but I want to preserve the data as well. When I
changed the database to postgres, all my history got lost. Is there any way
I can preserve the data in sqlite database while converting to postgres.

Regards
Harendra




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[galaxy-dev] problems with 'Profile Annotations' tool UI

[Hans-Rudolf Hotz]

Hi

we are looking into different methods to display dynamic contents in the 
tool user interface.


To start, we looked at the 'Operate on Genomic Intervals:Profile 
Annotations' tool. We turned it on in a local installation (May 20, 
8c11dd28a3cf release), but we struggled to get the interface to work.



On 'http://main.g2.bx.psu.edu/', the tables to choose from are only 
displayed if there is a history item with: format: bed, database: hg18.


But in our local test installation, we don't get the list of tables, no 
matter whether we have a ('hg18') bed file in our history or not. It 
looks like as if the 'from_file=annotation_profiler_options.xml' 
statement in the annotation_profiler.xml is ignored.


I know, the file 'annotation_profiler_options.xml' is read, since I get 
an error during restart, if I provide invalid xml.


Is there anything else, I have to enable, in order to get this interface 
to work? Currently, I don't care about the tools functionality, I just 
want the (cool) interface to work.



Thank you very much for your help.


Regards, Hans



PS: this question is connected to Tim's question yesterday - I just
should have sent mine first - sorry.
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Re: [galaxy-dev] bowtie on localgalaxy

[Hans-Rudolf Hotz]

On 06/09/2011 02:47 PM, Arun Selvam wrote:

Hi,

I am new to galaxy, I just downloaded and installed galaxy on my MAC

 system. I also download bowtie , and it is working perfectly on the
 command line. But am not able to see the bowtie option under mapping
 in the galaxy menu.

Are you sure, you did not comment'out it in the 'tool_conf.xml'?

Do you get an error in the log file after restart, following the line:

galaxy.tools DEBUG 2011-06-09 15:08:52,316 Loaded tool: bowtie_wrapper 1.1.2



Regards, Hans



 Do I have to do another modifications like move into particular folder
 or create some files or set path ? Could anyone please help me on this ?


Thank you

Arun




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Re: [galaxy-dev] rpy and R

[Hans-Rudolf Hotz]

Hi Ryan

Our sysadmin spent quite some time on this problem...in the end, he gave 
up and installed R 2.9.0 on our new server.


So, we ended up with two versions of R: one is used for rpy (we define:
R_HOME=/***/***/galaxy/helpers/R/R-2.9.0 in the 'run.sh' script), and 
an up-to-date version of R (ie 2.13.0) is used to execute our self 
written Rscripts, which we have added.



Regards, Hans


On 06/22/2011 01:43 AM, Ryan Davis wrote:


Hi all,

I'm currently working on setting up a Galaxy on our local server. I'm going
through the tool dependencies list and install everything on it. I
installed the latest R version (2.12.2) and now I'm trying to install rpy
1.0.3.

I have installed R with --enable-R-shlib and also done this step:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/R/lib/

However I get the following error with the install of rpy 1.0.3.

Thanks for the help,

Ryan

[cgtepper@hobbes rpy-1.0.3]$ python setup.py install
RHOMES= []
DEBUG= True
Setting RHOMES to  ['/usr/lib64/R']
### Using R verion 2.12.2 installed at /usr/lib64/R ###
RHOME= /usr/lib64/R
copying src/rpymodule.c -  src/rpymodule2122.c
copying src/R_eval.c -  src/R_eval2122.c
copying src/io.c -  src/io2122.c
running install
running build
running build_py
running build_ext
building '_rpy2122' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DRPY_SHNAME=_rpy2122 -DINIT_RPY=init_rpy2122
-UPRE_2_2 -UWITH_NUMERIC -I/usr/lib64/R/include -Isrc
-I/usr/share/R/include -I/usr/local/include/python2.6 -c
src/rpymodule2122.c -o build/temp.linux-x86_64-2.6/src/rpymodule2122.o -shared
src/rpymodule2122.c:42:23: error: Rversion.h: No such file or directory
src/rpymodule2122.c:43:28: error: missing binary operator before token (
In file included from src/rpymodule2122.c:51:
src/RPy.h:51:15: error: R.h: No such file or directory
src/RPy.h:52:22: error: Rdefines.h: No such file or directory
src/RPy.h:53:24: error: Rinternals.h: No such file or directory
src/RPy.h:57:28: error: R_ext/Rdynload.h: No such file or directory
src/RPy.h:58:29: error: R_ext/eventloop.h: No such file or directory
In file included from src/RPy.h:71,
  from src/rpymodule2122.c:51:
src/rpy_Rinterface.h:51:27: error: R_ext/Boolean.h: No such file or directory
In file included from src/rpy_Rinterface.h:61,
  from src/RPy.h:71,
  from src/rpymodule2122.c:51:
src/rpy_Startup.h:70: error: expected specifier-qualifier-list before
‘Rboolean’
In file included from src/RPy.h:71,
  from src/rpymodule2122.c:51:
src/rpy_Rinterface.h:70: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘R_Interactive’
src/rpy_Rinterface.h:71: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘R_Quiet’
src/rpy_Rinterface.h:72: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘R_Slave’
src/rpy_Rinterface.h:73: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘R_Verbose’
src/rpy_Rinterface.h:76: error: expected declaration specifiers or ‘...’
before ‘Rboolean’
src/rpy_Rinterface.h:85: warning: function declaration isn’t a prototype
src/rpy_Rinterface.h:96: warning: function declaration isn’t a prototype
src/rpy_Rinterface.h:101: warning: function declaration isn’t a prototype
src/rpy_Rinterface.h:102: warning: function declaration isn’t a prototype
src/rpy_Rinterface.h:103: warning: function declaration isn’t a prototype
src/rpy_Rinterface.h:112: warning: parameter names (without types) in
function declaration
In file included from src/rpymodule2122.c:51:
src/RPy.h:77:51: error: Rdevices.h: No such file or directory
In file included from src/RPy.h:108,
  from src/rpymodule2122.c:51:
src/robjobject.h:47: error: expected specifier-qualifier-list before ‘SEXP’
src/robjobject.h:62: error: expected ‘)’ before ‘int’
In file included from src/rpymodule2122.c:51:
src/RPy.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘to_Robj’
src/RPy.h:116: warning: parameter names (without types) in function declaration
src/RPy.h:117: warning: parameter names (without types) in function declaration
src/RPy.h:118: error: expected ‘)’ before ‘int’
src/RPy.h:129: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘do_eval_expr’
src/RPy.h:130: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘do_eval_fun’
src/RPy.h:131: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘get_fun_from_name’
src/RPy.h:208: error: expected ‘)’ before ‘robj’
src/RPy.h:209: error: expected ‘)’ before ‘robj’
src/RPy.h:210: error: expected ‘)’ before ‘robj’
src/RPy.h:211: error: expected ‘)’ before ‘robj’
src/rpymodule2122.c:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘get_item’
src/rpymodule2122.c:78: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘set_item’
src/rpymodule2122.c:79: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘length’

Re: [galaxy-dev] manage data libraries -menu upload files from filesystem paths not present

[Hans-Rudolf Hotz]

Hi Colin

In your 'universe_wsgi.ini' file, have you changed the line:

library_import_dir = None

to the directory with your data?


Regards, Hans



On 06/28/2011 11:38 AM, colin wrote:

Hi,
i all, my first post in the mailing list. I started one moth ago galaxy (at the 
conference) and the tool is really impressive. thx for it.
I installed a local version of galaxy (http://ampere.ulb.ac.be), but i am 
having some trouble when uploading private data on it.

Here is the procedure i followed:
1/ I got sra samples from ncbi:
http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546

2/ i transformed these sra in fastq format using the sratoolkit
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
--  this provides me fastq files of 25Gb

3/ PROBLEMS:
a/ IF I try to upload the data set using an URL in upload file
(I created a controller here: 
http://insilico.ulb.ac.be/publicutilities/sendonthefly?url=/fs1-ampere/GenomicsData/ERP000546/ERR030856.fastq)
then only 155Mb are uploaded to galaxy (and no error)

b/ if i try to follow that method: 
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
and i try to get data from the server, the menu upload files from filesystem paths and 
upload directory of files are not present.
==  no way to access these files locally


any hints for that?

thx
Colin



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Re: [galaxy-dev] manage data libraries -menu upload files from filesystem paths not present

[Hans-Rudolf Hotz]

On 06/28/2011 01:50 PM, colin molter wrote:

hi,

no, i found that just later and that solved the problem. i wanted to cancel
my question .. but too late.
anyway i managed to put my 35Gb fastq files on galaxy and i am transforming
it whith the fastq groomer.

any idea about the other problem (upload using url)? which stopped at 155Mb
with no error?


No, I just guess it is a browser issue, hence for big files, upload via 
ftp is recommended, see:


https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP


Hans



thx again
colin

2011/6/28 Hans-Rudolf Hotzh...@fmi.ch


Hi Colin

In your 'universe_wsgi.ini' file, have you changed the line:

library_import_dir = None

to the directory with your data?


Regards, Hans




On 06/28/2011 11:38 AM, colin wrote:


Hi,
i all, my first post in the mailing list. I started one moth ago galaxy
(at the conference) and the tool is really impressive. thx for it.
I installed a local version of galaxy (http://ampere.ulb.ac.be), but i am
having some trouble when uploading private data on it.

Here is the procedure i followed:
1/ I got sra samples from ncbi:
http://trace.ncbi.nlm.nih.gov/**Traces/sra/?study=ERP000546http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546

2/ i transformed these sra in fastq format using the sratoolkit
https://bitbucket.org/galaxy/**galaxy-central/wiki/**
DataLibraries/UploadingFileshttps://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
--   this provides me fastq files of 25Gb

3/ PROBLEMS:
a/ IF I try to upload the data set using an URL in upload file
(I created a controller here: http://insilico.ulb.ac.be/**
publicutilities/sendonthefly?**url=/fs1-ampere/GenomicsData/**
ERP000546/ERR030856.fastqhttp://insilico.ulb.ac.be/publicutilities/sendonthefly?url=/fs1-ampere/GenomicsData/ERP000546/ERR030856.fastq
)
then only 155Mb are uploaded to galaxy (and no error)

b/ if i try to follow that method: https://bitbucket.org/galaxy/**
galaxy-central/wiki/**DataLibraries/UploadingFileshttps://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
and i try to get data from the server, the menu upload files from
filesystem paths and upload directory of files are not present.
==   no way to access these files locally


any hints for that?

thx
Colin



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Re: [galaxy-dev] Fail to start galaxy

[Hans-Rudolf Hotz]

Hi Colin


I launched a big job on my local galaxy server (for which I am admin). The job 
was to put local dir in the datalist.
It took too long and i wanted to stop it  but how?? i failed to find a 
solution.


go to the admin view - 'Manage jobs' and there you can kill individual 
jobs.



To stop the job i thought that stopping the galaxy running instance could make 
it. (AM I RIGHT?)


possible, but sounds like an 'overkill' to me. I would first try the 
'soft' method described aboveand use this only as a last resort.



Unfortunately, i failed to restart galaxy. I have the following error:



are you sure you have killed the galaxy process? Since this part of the 
error message tells me that Galaxy (or another service) is still using 
the port number.


 socket.error: (98, 'Address already in use')


How did you stop galaxy?



Regards, Hans
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Re: [galaxy-dev] Fail to start galaxy

[Hans-Rudolf Hotz]

On 06/28/2011 07:06 PM, colin molter wrote:

hi hans,
you are right.
it seems that even if i stopped galaxy
(i just stopped the run.sh command)

i still have a job running:
root 10441 97.0  0.0  77496  1772 pts/6R11:59 402:48 python
/opt/galaxy-central/tools/fastq/fastq_groomer.py /fs1/GenomicsData/ERP0005

it seems that the transformation of a fastq file is taking a lot of time (it
uses 100%of cpu since 7hours).
does it sound normal?



I am not very familiar with 'fastq_groomer.py' and without knowing the 
size of your fasta file, it is impossible to tell.


Have you tried a subset of your fasta file? May be your data is corrupt 
resulting in an endless loop?



Hans



i think i have better to kill that job and to try another way.

i stopped the job and it works
thx.


2011/6/28 Hans-Rudolf Hotzh...@fmi.ch


Hi Colin


  I launched a big job on my local galaxy server (for which I am admin). The

job was to put local dir in the datalist.
It took too long and i wanted to stop it  but how?? i failed to find a
solution.



go to the admin view -  'Manage jobs' and there you can kill individual
jobs.


  To stop the job i thought that stopping the galaxy running instance could

make it. (AM I RIGHT?)



possible, but sounds like an 'overkill' to me. I would first try the 'soft'
method described aboveand use this only as a last resort.


  Unfortunately, i failed to restart galaxy. I have the following error:




are you sure you have killed the galaxy process? Since this part of the
error message tells me that Galaxy (or another service) is still using the
port number.



socket.error: (98, 'Address already in use')



How did you stop galaxy?



Regards, Hans






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Re: [galaxy-dev] Refreshing/Reloading Files

[Hans-Rudolf Hotz]

Hi Paul

You probably need to be a bit more specific...at what stage is this 
'.txt file' read (or rather should be read)? - are you offering the 
(growing) list of databases as options to select in the GUI?


Hans


On 06/29/2011 10:20 AM, Admins de Galaxy wrote:

Hello everyone,
we have a problem with one of our selfwritten tools.
We have a tool, that compares sequence with a database.
The List of the available databases is  loaded from a .txt file.

One of our other tools, manages that a new database is
added to the .txt file. But Galaxy doesn't recognize the change.

It would be nice if someone could give us an advice.

Best regards

Paul K. Deuster
@ Technische Hochschule Mittelhessen




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Re: [galaxy-dev] Refreshing/Reloading Files

[Hans-Rudolf Hotz]

Hi Paul

Please keep all replies on the list by using reply all


A simple solution, which we use quite a lot, is the following:


we use the dynamic_options attribute, eg:



 inputs
param name=foo type=select label=what
   help=Use tickboxes to select 
   display=radio
   dynamic_options=ds_fooOptions()/
  /inputs
  outputs
data format=fasta name=output label=more foo /

  /outputs
  code file=extra_code_for_foo_list.py /
   help
   /help

 /tool


and then we have a little python script (extra_code_for_foo_list.py) 
with the ds_fooOptions function, which can read your file (ie your 
list of databases), eg



def ds_fooOptions():
List available foos as tuples of (displayName,value)
foos = whatever python code is required to generate the tuples
return foos



I hope this helps, Hans



On 06/29/2011 08:09 PM, Admins de Galaxy wrote:

Hi Hans,

yes that's it. We are offering the list of databases as options to select in
the GUI,
  before executing the script which compares the selected database with the
sequence.

Paul

2011/6/29 Hans-Rudolf Hotzh...@fmi.ch


Hi Paul

You probably need to be a bit more specific...at what stage is this '.txt
file' read (or rather should be read)? - are you offering the (growing) list
of databases as options to select in the GUI?

Hans



On 06/29/2011 10:20 AM, Admins de Galaxy wrote:


Hello everyone,
we have a problem with one of our selfwritten tools.
We have a tool, that compares sequence with a database.
The List of the available databases is  loaded from a .txt file.

One of our other tools, manages that a new database is
added to the .txt file. But Galaxy doesn't recognize the change.

It would be nice if someone could give us an advice.

Best regards

Paul K. Deuster
@ Technische Hochschule Mittelhessen




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Re: [galaxy-dev] problems with 'Profile Annotations' tool UI

[Hans-Rudolf Hotz]

Hi Dan

Thank you very much. The display works nicely, now.

Thanks, Hans


On 07/07/2011 06:14 PM, Daniel Blankenberg wrote:

Hi Hans,

Very sorry for the delay in response.  The sample file that was included was 
incorrect, but has been updated in changeset 5775:4220f8a5c571 and should now 
display an interface.

If you would like to use or run the tool, you may find 
$GALAXY_ROOT/scripts/tools/annotation_profiler/README.txt helpful. Please let 
us know if you encounter further difficulties.

Thanks for using Galaxy,

Dan


On Jun 8, 2011, at 8:10 AM, Hans-Rudolf Hotz wrote:


Hi

we are looking into different methods to display dynamic contents in the tool 
user interface.

To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We 
turned it on in a local installation (May 20, 8c11dd28a3cf release), but we 
struggled to get the interface to work.


On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is 
a history item with: format: bed, database: hg18.

But in our local test installation, we don't get the list of tables, no matter whether we have a 
('hg18') bed file in our history or not. It looks like as if the 
'from_file=annotation_profiler_options.xml' statement in the 
annotation_profiler.xml is ignored.

I know, the file 'annotation_profiler_options.xml' is read, since I get an 
error during restart, if I provide invalid xml.

Is there anything else, I have to enable, in order to get this interface to 
work? Currently, I don't care about the tools functionality, I just want the 
(cool) interface to work.


Thank you very much for your help.


Regards, Hans



PS: this question is connected to Tim's question yesterday - I just
should have sent mine first - sorry.
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Re: [galaxy-dev] new data type.

[Hans-Rudolf Hotz]

Hi Luobin

It is difficult to guess without seeing your code.

So, assuming you followed the steps described in the wiki 
(http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes), I guess 
you just made a typo somewhere (since this has happen to me several 
times when adding a new datatype). Have you double checked your tool 
definition file?



Regards, Hans


On 07/22/2011 07:52 AM, Luobin Yang wrote:

Hi,

I created an XML file for a tool. This tool has an Nexus input. When I click
the input field of the web interface for this tool, it shows all kinds of
data that I can select. How do I restrict the list to show only data in
nexus format? I added a line in the registration part and the sniffer part
of the datatypes_conf.xml and I also created a class called Nexus which
inherits the class galaxy.datatypes.Sequence, but this doesn't solve the
problem.

Thanks,
Luobin




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[galaxy-dev] problems with Access Libraries stored locally tool

[Hans-Rudolf Hotz]

Hi

I apologize, if this problem has already been solved/discussed. I went 
through the e-mail repos, but couldn't find anything.



With a little delay, I am in the process of upgrading our local Galaxy 
server. Currently, I am running a few tests with the June 23, 2011 
(720455407d1c) release.



I noticed the following problem during start-up of a fresh download:

galaxy.tools DEBUG 2011-08-16 16:15:06,567 Loading section: SNP/WGA: 
Data; Filters

galaxy.tools DEBUG 2011-08-16 16:15:06,630 Loaded tool: upload1 1.1.3
galaxy.tools ERROR 2011-08-16 16:15:06,639 error reading tool from path: 
data_source/access_libraries.xml

Traceback (most recent call last):
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, 
line 77, in load_tool

tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, 
line 169, in load_tool

return ToolClass( config_file, root, self.app )
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, 
line 340, in __init__

self.parse( root )
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, 
line 385, in parse

self.interpreter = command.get(interpreter, None)
AttributeError: 'NoneType' object has no attribute 'get'
galaxy.tools DEBUG 2011-08-16 16:15:06,687 Loaded tool: rgClean1 1.0.0


and as a consequence: the tool Access Libraries stored locally is not 
available. Does anybody know, what went wrong?   -  The __init__.py is 
a little bit too big of a beast for me   ;)



We use this tool quite a lot for general access to data libraries (in 
addition to the drop down in the top menu bar)


Thank you very much for any help

Regards, Hans
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Re: [galaxy-dev] problems with Access Libraries stored locally tool

[Hans-Rudolf Hotz]

Hi Greg

Thank you very much for you help.

I managed to fix '~/lib/galaxy/tools/__init__.py'  manually according 
the diff in your changeset, and it is working fine.


Regards, Hans





On 08/16/2011 05:01 PM, Greg Von Kuster wrote:

Hans,

This bug was fixed in the following change set - not sure if it is currently 
available in the distribution.  If not, it should be within the next few weeks. 
 If you need it sooner, you'll have to pull from our development repo at 
http://bitbucket.org/galaxy/galaxy-central/

0f15591f2acdFix for tool configs that do not include a command tag.
Branch
25 days ago



On Aug 16, 2011, at 10:38 AM, Hans-Rudolf Hotz wrote:


Hi

I apologize, if this problem has already been solved/discussed. I went through 
the e-mail repos, but couldn't find anything.


With a little delay, I am in the process of upgrading our local Galaxy server. Currently, 
I am running a few tests with the June 23, 2011 (720455407d1c) release.


I noticed the following problem during start-up of a fresh download:

galaxy.tools DEBUG 2011-08-16 16:15:06,567 Loading section: SNP/WGA: Data; 
Filters
galaxy.tools DEBUG 2011-08-16 16:15:06,630 Loaded tool: upload1 1.1.3
galaxy.tools ERROR 2011-08-16 16:15:06,639 error reading tool from path: 
data_source/access_libraries.xml
Traceback (most recent call last):
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, line 77, 
in load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, line 
169, in load_tool
return ToolClass( config_file, root, self.app )
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, line 
340, in __init__
self.parse( root )
  File /galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py, line 
385, in parse
self.interpreter = command.get(interpreter, None)
AttributeError: 'NoneType' object has no attribute 'get'
galaxy.tools DEBUG 2011-08-16 16:15:06,687 Loaded tool: rgClean1 1.0.0


and as a consequence: the tool Access Libraries stored locally is not available. Does 
anybody know, what went wrong?   -  The __init__.py is a little bit too big of a beast 
for me   ;)


We use this tool quite a lot for general access to data libraries (in addition 
to the drop down in the top menu bar)

Thank you very much for any help

Regards, Hans
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu





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[galaxy-dev] Could not save visualization error with June 23, 2011 release

[Hans-Rudolf Hotz]

Hi

I am pretty sure, this must have been discussed before, but again, I 
cannot find a hint/reference in the e-mail archive:



If I install a new galaxy server using the  June 23, 2011 release 
(changeset: 5743:720455407d1c), I cannot save a visualization after 
adding a new track:


I get a little pop-up window saying Could not save visualization, if I 
click on 'ok' it pretends to start saving, but the web browser freezes.



and I get the following error:

URL: http://silicon.fmi.ch:8097/tracks/save
File 
'/galaxy/galaxy_test/galaxy_dist/eggs/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', 
line 364 in respond

  app_iter = self.application(environ, detect_start_response)
File 
'/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', 
line 98 in __call__

  environ, self.app)
File 
'/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', 
line 539 in intercept_output

  app_iter = application(environ, replacement_start_response)
File 
'/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', 
line 80 in __call__

  return self.application(environ, start_response)
File 
'/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', 
line 632 in __call__

  return self.application(environ, start_response)
File '/galaxy/galaxy_test/galaxy_dist/lib/galaxy/web/framework/base.py', 
line 145 in __call__

  body = method( trans, **kwargs )
File 
'/galaxy/galaxy_test/galaxy_dist/lib/galaxy/web/framework/__init__.py', 
line 65 in decorator

  return simplejson.dumps( func( self, trans, *args, **kwargs ) )
File 
'/galaxy/galaxy_test/galaxy_dist/lib/galaxy/web/controllers/tracks.py', 
line 580 in save

  track_type: track['track_type'],
KeyError: 'track_type'


Is this a 'bug' in the  June 23, 2011 release ?


By looking through the commits on galaxy central i found the 'changeset: 
5750:b13d16085dfc' from Jun 27: Add generic method for getting track 
type and use it when saving visualizations.


I am now using the two 'fixed' files:
~/static/scripts/trackster.js
~/templates/tracks/browser.mako


and it now seems to work, ie I can save the changed visualization.


Was this the right fix?



Thank you very much for your help
Regards, Hans
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[galaxy-dev] trackster problem with IE8 and IE7 when using June 23, 2011 release

[Hans-Rudolf Hotz]

Hi

I am sorry to be a pain in the neck, but as part of our quarterly 
upgrade procedure, I am stumbling across the next problem:


Can anybody confirm, that the visualization does not work with the
June 23, 2011 release (changeset: 5743:720455407d1c) when using  IE8 
or IE7 on windows XP?


(it works with chrome and firefox6 on windows XP, and no problems with 
mac and linux)



And like the previous problems, is there a quick fix available?


Thank you very much for your help
Regards, Hans
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Re: [galaxy-dev] creating new input/output formats

[Hans-Rudolf Hotz]

On 08/25/2011 12:12 PM, Nikhil Joshi wrote:

Hi all,

Is there a relatively easy way to create your own input/output formats?
Some of the formats from programs that I am trying to install on our local
Galaxy do not exist as an option.  Any ideas?



Hi

have you looked at the following wiki page:

http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes



Regards, Hans


- Nik.







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[galaxy-dev] filtering BED files by score in trackster

[Hans-Rudolf Hotz]

Hi

The option to filter a BED file by the score in the visualization tool 
is brilliant! There is just one draw back: you can only filter by 
integers. Hence a score of 1.1 is the same as of score of 1.3.


How difficult would it be to change the code in order to allow floats 
for the filter?  Such a feature would help us a lot!


I tried to dig into the visualization code...but I got lost.

Thank you very much for your help


Regards, Hans
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Re: [galaxy-dev] EST download from any source?

[Hans-Rudolf Hotz]

On 09/14/2011 10:39 AM, Timothy Wu wrote:

//


Alternatively, I can just ask user to download from NCBI ftp themselves,
decompress them, and upload it to galaxy.

What's the best approach here?


How about: you download the data once, and then offer it as a 'data 
library' to your users. This way you avoid data duplication.




And I noticed that file types does not include genbank types nor gzip
types. Is there some generic type I could use? Just Data class?


We treat GenBank files as txt. This works fine with the EMBOSS tools.

Regards, Hans




Timothy


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Re: [galaxy-dev] strange history error

[Hans-Rudolf Hotz]

Hi

just asking the obvious questions to double check:

 - are you sure, this second instance is not accessing the same
   PostgreSQL/MySQL database as the first one?

 - are you sure, the user you are logged-in does exist in the
   PostgreSQL/MySQL database? I kind of remember getting a similar
   error after switching to external authentication. The
   difference was due to capitalization in parts of the e-mail address.


Regards, Hans


On 10/12/2011 01:39 AM, Chorny, Ilya wrote:

I am getting a strange error that I cannot figure out how to debug. It's from a 
second instance we have running on the same server.  When I upload data it does 
not show me my history. I get the following messages from the log file. 
Thoughts?

galaxy.web.framework DEBUG 2011-10-11 15:47:50,259 Error: this request returned 
None from get_history(): 
http://ussd-dev-swim02.illumina.com/galaxy2/history/list
galaxy.web.framework DEBUG 2011-10-11 15:47:50,261 Error: this request returned 
None from get_history(): 
http://ussd-dev-swim02.illumina.com/galaxy2/history/list
galaxy.web.framework DEBUG 2011-10-11 16:34:25,717 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,717 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,719 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,719 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create

Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.commailto:icho...@illumina.com
Website: www.illumina.comhttp://www.illumina.com





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Re: [galaxy-dev] Name your own tool's output?

[Hans-Rudolf Hotz]

Hi Timothy

Are you talking about the name as it will appear in the history?

Then have a look at the following wiki page:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set



Regards, Hans

On 10/12/2011 10:50 AM, Timothy Wu wrote:

Hi,

I thought I had already asked this question a while ago, but I can't find it
so I guess I haven't.

When porting my own tool, is there anyway to customize the name of the
output?

Timothy




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[galaxy-dev] second question, Re: Name your own tool's output?

[Hans-Rudolf Hotz]

Hi Timothy


I don't really see the connection to you first question, but maybe I 
misunderstood the first one


Anyway, you probably need to define those output files which are 
required by B as 'Static Multiple Outputs' and the rest as 'Variable 
Static Outputs determined by parameter values'. Again, see the wiki:


http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files


Regards, Hans






On 10/12/2011 11:02 AM, Timothy Wu wrote:

On Wed, Oct 12, 2011 at 4:50 PM, Timothy Wu2hug...@gmail.com  wrote:


Hi,

I thought I had already asked this question a while ago, but I can't find
it so I guess I haven't.

When porting my own tool, is there anyway to customize the name of the
output?

Timothy



I have another perhaps related question. If my tool A have variable number
of outputs no known till tool run, but the next tool B in pipeline requires
a couple of designated outputs (not all) from tool A, is there a way to
specify this in the workflow? In another word, A has various different type
of output, and I want some output file from A to go into this particular
input file field in B.

I though this might be related to my prior question.

Timothy




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Re: [galaxy-dev] updating configuration files after code update

[Hans-Rudolf Hotz]

Hi Andrew

you might wanna look at the Config files listed in the '.hgignore' file.

I usually do a quick diff on the new *.sample file with a copy of the 
previous file and then merge any required changes into the actual file.


Regards, Hans


On 10/25/2011 10:38 PM, Andrew Warren wrote:

When first running Galaxy there are a number of files that are created
including universe_wsgi.ini.  After doing an 'hg pull -u' the sample
version of this file will be updated but not the specific server
instance of the file that was initially created.

I was wondering if there are any other files like this that need to be
updated/merged/replaced as development continues?
Also, does anyone have any good practices or methods for updating
configuration files? (right now I'm just using a visual diff and merge
to get the new options for universe_wsgi.ini)

Sorry if this has been covered somewhere or asked before, I couldn't
find any material on it.

Thanks,
Andrew Warren


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Re: [galaxy-dev] displaying dataset paths in the UI

[Hans-Rudolf Hotz]

Hi Shantanu


Sorry, for replying so late (I am working down a pile of e-mails which 
accumulated during my holidays).


I have just implemented your suggested changes in our dev server. It is 
brilliant - Thank you very much!


I will do it for our production server within the next few days.

Regards, Hans


On 10/20/2011 08:19 PM, Shantanu Pavgi wrote:


I am trying to display dataset paths in the UI when user clicks on the 'view 
details' icon in the history panel. I was able to display it by adding 
'hda.file_name' field in the show_params.mako template file and it seems to be 
working. Following is a diff for it:

{{{
diff --git a/templates/show_params.mako b/templates/show_params.mako
index 9f7ad36..58d8108 100644
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -50,6 +50,8 @@
  trtdDbkey:/tdtd${hda.dbkey}/td/tr
  trtdFormat:/tdtd${hda.ext}/td/tr
  trtdTool Version:/tdtd${hda.tool_version}/td/tr
+trtdDataset ID:/tdtd${hda.dataset_id}/td/tr
+trtdDataset Path:/tdtd${hda.file_name}/td/tr
  /table
  br /
  table class=tabletip
}}}

It doesn't display any metadata files associated with the dataset. I guess it 
will need some more changes in the datasets controller to return metadata file 
paths to this template. But, are these right places to make changes for 
displaying dataset paths or are there any other files/modules that should be 
modified? Any comments or suggestions for implementing this will be really 
helpful.

--
Thanks,
Shantanu.

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Re: [galaxy-dev] Running galaxy on external hard drive

[Hans-Rudolf Hotz]

Hi Allessia


It is difficult to help you without knowing what kind of error you've 
got.


What is the error message you get?


Regards, Hans


On 10/31/2011 03:35 PM, Alessia D wrote:

Hi,

I am very new to Galaxy and so far have only used the online interface.
  However, I have an old Unix-running computer and I was hoping to run
Galaxy as a local instance.  However, the computer has a very small hard
drive, that is already half full, so I was wondering if there is any way I
can run Galaxy by installing it on an external hard drive.  I tried
already, and was able to install it properly and connect, but I get errors
when I try to upload data.

Any help would be greatly appreciated.  I don't have a lot of experience
with Unix systems, so it might be something easy to solve or impossible to
do, I have no idea.

Thanks!

Alessia




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Re: [galaxy-dev] Can not clean my galaxy datasets

[Hans-Rudolf Hotz]

Hi Liram

This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) 
database.


Before copying your existing Galaxy server, you might wanna start with 
running a second Galaxy server in parallel using a fresh check-out.


Regards, Hans


Have you tried to run a

On 12/19/2011 04:08 PM, Jennifer Jackson wrote:



On 12/19/11 6:15 AM, liram_va...@agilent.com wrote:

Hi Jennifer,

Thank you again for the quick reply in my last issue.

I have another Galaxy problem and I hope you will be able to assist.
Because I am developing my Galaxy server while there are members in my
group that are using this Galaxy instance in parallel,
I am trying to create another Galaxy process (instance), which will be
used only for testing...

Therefore, I created a copy of Galaxy directory in other location (let
say: /galaxy-dist_test)
And changed the listening port in universe_wsgi.ini to another port
(8081).
Then, I tried to run both of Galaxy instances in parallel.
(One is listening on port 8080 and the other is on 8081)

The problem is occurred when I send a job for a run in one of the
instance (let say: the one that run on 8080),
Then, It cause to the another Instance (the one on port 8081) to
collapse (And the history is disappeared...)

What is the problem?
How can I solve it?
How can I create two different and self-contained galaxy servers on
the same computer?

I tried also to use the instructions :
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling

But it was not helpful to my problem...

Thank you a lot!
Liram

-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, November 29, 2011 4:42 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Can not clean my galaxy datasets

Hello Liram,

Perhaps the allow_user_dataset_purge option has not been set to True
in universe_wsgi.ini?

Please see this wiki for details:
http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas

Hopefully this helps, but please let us know if you need more assistance,

Best,

Jen
Galaxy team

On 11/29/11 5:44 AM, liram_va...@agilent.com wrote:

Hello,

My name is Liram Vardi and I'm using local Galaxy instance.

Anyway, I can't clean my deleted datasets from my own locally disk.

When I am trying to delete dataset, as was explained in
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,

First, I used the delete 'X' icon near the dataset to delete the
dataset,

Then, when I go to Options - Show Deleted Datasets, I can see my
deleted dataset on the list

with the note: /This dataset has been deleted. Click _here_ to
undelete it//*but I don't get the also the option or _here_ to
immediately remove it from disk.*/.

Also, when I use the option Options - Purge Deleted Datasets, I'm
getting a message 0 datasets have been deleted permanently and

my deleted dataset still stays in the Options - Show Deleted Datasets
menu list.

I also tried to clear the history, but when I'm doing that, the using
X Mb tab on the upper right corner is still not reset.

What is the problem?

Thanks a lot for your help!

Liram



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support




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[galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets

[Hans-Rudolf Hotz]

Hi Liram

I was suggesting: instead of copying the existing Galaxy directory into 
another location. Download and install a new Galaxy installation in a 
separate location on your file system.


for the installation procedure, see:

http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy

all you need to do in the new installation is changing the port number. 
It will create its own file system and by default it will use its own 
SQLite database. Hence, there should be no interference with your 
existing, production Galaxy installation.


Regards, Hans


On 12/21/2011 09:16 AM, liram_va...@agilent.com wrote:

Hi Hans,

Thank you for your quick reply.

Sorry, But I'm a rookie Galaxy user,
So may you pls explain me in details the meaning by  running a second Galaxy server 
in parallel using a fresh check-out ?
Thank a lot for your assistance!

Liram

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Monday, December 19, 2011 7:01 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1)
Subject: Re: [galaxy-dev] Can not clean my galaxy datasets

Hi Liram

This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.

Before copying your existing Galaxy server, you might wanna start with running 
a second Galaxy server in parallel using a fresh check-out.

Regards, Hans


Have you tried to run a

On 12/19/2011 04:08 PM, Jennifer Jackson wrote:



On 12/19/11 6:15 AM, liram_va...@agilent.com wrote:

Hi Jennifer,

Thank you again for the quick reply in my last issue.

I have another Galaxy problem and I hope you will be able to assist.
Because I am developing my Galaxy server while there are members in
my group that are using this Galaxy instance in parallel, I am trying
to create another Galaxy process (instance), which will be used only
for testing...

Therefore, I created a copy of Galaxy directory in other location
(let
say: /galaxy-dist_test)
And changed the listening port in universe_wsgi.ini to another port
(8081).
Then, I tried to run both of Galaxy instances in parallel.
(One is listening on port 8080 and the other is on 8081)

The problem is occurred when I send a job for a run in one of the
instance (let say: the one that run on 8080), Then, It cause to the
another Instance (the one on port 8081) to collapse (And the history
is disappeared...)

What is the problem?
How can I solve it?
How can I create two different and self-contained galaxy servers on
the same computer?

I tried also to use the instructions :
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%
20Scaling

But it was not helpful to my problem...

Thank you a lot!
Liram

-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, November 29, 2011 4:42 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Can not clean my galaxy datasets

Hello Liram,

Perhaps the allow_user_dataset_purge option has not been set to True
in universe_wsgi.ini?

Please see this wiki for details:
http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas

Hopefully this helps, but please let us know if you need more
assistance,

Best,

Jen
Galaxy team

On 11/29/11 5:44 AM, liram_va...@agilent.com wrote:

Hello,

My name is Liram Vardi and I'm using local Galaxy instance.

Anyway, I can't clean my deleted datasets from my own locally disk.

When I am trying to delete dataset, as was explained in
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,

First, I used the delete 'X' icon near the dataset to delete the
dataset,

Then, when I go to Options -  Show Deleted Datasets, I can see my
deleted dataset on the list

with the note: /This dataset has been deleted. Click _here_ to
undelete it//*but I don't get the also the option or _here_ to
immediately remove it from disk.*/.

Also, when I use the option Options -  Purge Deleted Datasets, I'm
getting a message 0 datasets have been deleted permanently and

my deleted dataset still stays in the Options -  Show Deleted Datasets
menu list.

I also tried to clear the history, but when I'm doing that, the
using X Mb tab on the upper right corner is still not reset.

What is the problem?

Thanks a lot for your help!

Liram



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support




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Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets

[Hans-Rudolf Hotz]

On 12/22/2011 11:46 AM, liram_va...@agilent.com wrote:

Hi Hans,

Thank you for your reply.
Anyway, I tried to install Galaxy again by using the site check-out (hg clone 
https://...)  and it still cause problems.

Specifically, those were my steps:
1) I Installed galaxy in different location.
2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on 
different port.


It is hard to believe that your new test installation running with 
SQLite interferes with your existing installation running with 
PostgreSQL(?). Are you sure, there is not a third 'party' involved?


Also, I would stop at this step (ie: changed universe_wsgi.ini to listen 
on different port) and run your installation first like this. And wait 
with copying anything from the exiting code or data or directories. Till 
you manage to get the two web site to run in parallel without 
interfering with each other.



Regards, Hans






3) Manually, I copied tools and tool-data directories from the old instance 
of Galaxy to the new location (In order to get my new tools).
4) Also, I copied the old config tool file:  tool_conf.xml
5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already on 
line.

The problem is that any operation on the new Galaxy instance cause to the other 
Galaxy to
Throw the following error message:

URL: http://ip address.../user/login?use_panels=False
File 
'/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
 line 364 in respond
   app_iter = self.application(environ, detect_start_response)
File 
'/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', 
line 98 in __call__
   environ, self.app)
File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', 
line 539 in intercept_output
   app_iter = application(environ, replacement_start_response)
.
.
.
.
File 
'/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
 line 931 in _handle_dbapi_exception
   raise exc.DBAPIError.instance(statement, parameters, e, 
connection_invalidated=is_disconnect)
OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session 
SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 
10:27:05.978992', 0, 158]

I suppose that the problem is again caused due to collision between the 
databases.
But how can I separate between them?

Thanks you!!
Liram

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Wednesday, December 21, 2011 4:59 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: galaxy-...@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1)
Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] 
Can not clean my galaxy datasets

Hi Liram

I was suggesting: instead of copying the existing Galaxy directory into another 
location. Download and install a new Galaxy installation in a separate location 
on your file system.

for the installation procedure, see:

http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy

all you need to do in the new installation is changing the port number.
It will create its own file system and by default it will use its own SQLite 
database. Hence, there should be no interference with your existing, production 
Galaxy installation.

Regards, Hans


On 12/21/2011 09:16 AM, liram_va...@agilent.com wrote:

Hi Hans,

Thank you for your quick reply.

Sorry, But I'm a rookie Galaxy user, So may you pls explain me in
details the meaning by  running a second Galaxy server in parallel using a fresh 
check-out ?
Thank a lot for your assistance!

Liram

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Monday, December 19, 2011 7:01 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1)
Subject: Re: [galaxy-dev] Can not clean my galaxy datasets

Hi Liram

This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.

Before copying your existing Galaxy server, you might wanna start with running 
a second Galaxy server in parallel using a fresh check-out.

Regards, Hans


Have you tried to run a

On 12/19/2011 04:08 PM, Jennifer Jackson wrote:



On 12/19/11 6:15 AM, liram_va...@agilent.com wrote:

Hi Jennifer,

Thank you again for the quick reply in my last issue.

I have another Galaxy problem and I hope you will be able to assist.
Because I am developing my Galaxy server while there are members in
my group that are using this Galaxy instance in parallel, I am
trying to create another Galaxy process (instance), which will be
used only for testing...

Therefore, I created a copy of Galaxy directory in other location
(let
say: /galaxy-dist_test)
And changed the listening port in universe_wsgi.ini to another
port (8081).
Then, I tried to run both of Galaxy instances in parallel.
(One is listening on port 8080 and the other is on 8081)

The problem is occurred when I send a job for a run in one of the
instance (let say: the one

Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets

[Hans-Rudolf Hotz]

On 12/22/2011 04:13 PM, liram_va...@agilent.com wrote:

Hi Chris,

Thank you.
Just to make sure that I fully understand:
Basically you say that there are no easy way to run two Galaxy process on the 
same Linux operating system?



Hi Liram

I am sorry, but I can't leave this statement out there without strongly 
objecting!


I have been running up to 5 Galaxy servers (one production and four test 
servers) on the same box without any problems.



It is difficult to help you remotely, with only seeing snippets from 
your errors. But I am sure your local sysadmin can help you setting up 
the relational databases and making sure the file systems for your two 
servers are really separate from each other.


Hans




Thanks,
Liram

-Original Message-
From: Fields, Christopher J [mailto:cjfie...@illinois.edu]
Sent: Thursday, December 22, 2011 4:50 PM
To: Hans-Rudolf Hotz
Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-...@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1)
Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: 
Re: Can not clean my galaxy datasets

We are anticipating a similar issue and decided it would be easier to just have 
separate VMs where possible.  I know this isn't always possible, but it is a 
very easy way to both manage multiple galaxy instances and keep the various 
galaxy instances completely separate.

Chris

On Dec 22, 2011, at 6:10 AM, Hans-Rudolf Hotzh...@fmi.ch  wrote:




On 12/22/2011 11:46 AM, liram_va...@agilent.com wrote:

Hi Hans,

Thank you for your reply.
Anyway, I tried to install Galaxy again by using the site check-out (hg clone 
https://...)  and it still cause problems.

Specifically, those were my steps:
1) I Installed galaxy in different location.
2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on 
different port.


It is hard to believe that your new test installation running with SQLite 
interferes with your existing installation running with PostgreSQL(?). Are you 
sure, there is not a third 'party' involved?

Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on 
different port) and run your installation first like this. And wait with 
copying anything from the exiting code or data or directories. Till you manage 
to get the two web site to run in parallel without interfering with each other.


Regards, Hans






3) Manually, I copied tools and tool-data directories from the old instance 
of Galaxy to the new location (In order to get my new tools).
4) Also, I copied the old config tool file:  tool_conf.xml
5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already on 
line.

The problem is that any operation on the new Galaxy instance cause to
the other Galaxy to Throw the following error message:

URL: http://ip address.../user/login?use_panels=False
File 
'/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
 line 364 in respond
   app_iter = self.application(environ, detect_start_response) File
'/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', 
line 98 in __call__
   environ, self.app)
File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', 
line 539 in intercept_output
   app_iter = application(environ, replacement_start_response) .
.
.
.
File 
'/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
 line 931 in _handle_dbapi_exception
   raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
OperationalError: (OperationalError) database is locked u'UPDATE
galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id
= ?' ['2011-12-22 10:27:05.978992', 0, 158]

I suppose that the problem is again caused due to collision between the 
databases.
But how can I separate between them?

Thanks you!!
Liram

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Wednesday, December 21, 2011 4:59 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: galaxy-...@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1)
Subject: running two Galaxy installations on one server - was: Re:
[galaxy-dev] Can not clean my galaxy datasets

Hi Liram

I was suggesting: instead of copying the existing Galaxy directory into another 
location. Download and install a new Galaxy installation in a separate location 
on your file system.

for the installation procedure, see:

http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy

all you need to do in the new installation is changing the port number.
It will create its own file system and by default it will use its own SQLite 
database. Hence, there should be no interference with your existing, production 
Galaxy installation.

Regards, Hans


On 12/21/2011 09:16 AM, liram_va...@agilent.com wrote:

Hi Hans,

Thank you for your quick reply.

Sorry, But I'm a rookie Galaxy user, So may you pls explain me in
details the meaning by  running a second Galaxy server in parallel using a fresh 
check

Re: [galaxy-dev] (no subject)

[Hans-Rudolf Hotz]

On 01/09/2012 05:04 AM, Vidya .H.K wrote:

Hi,

I am new user to galaxy. I have installed galaxy on the Linux local server
for ChIP-seq analysis. While running MACS, an error is flagged
  An error occurred running this job: /bin/sh: macs: not found .
I have set the path for macs in /bin. But still the error persists. It
would be great if any one help me resolve this problem.



Hi Vidya

Is macs executable for the galaxy user (ie the user the galaxy server is 
running as) ?


Regards, Hans


Thanks in advance.


Regards
vidya



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Re: [galaxy-dev] (no subject)

[Hans-Rudolf Hotz]

On 01/10/2012 06:31 AM, Vidya .H.K wrote:

Hi,
I think macs is exceutable with galaxy user.





what happens if you execute macs_wrapper.py on the command line?

Regards, Hans


PS: Please send all follow-up with a cc to the mailing list (reply-all).



On 01/09/2012 05:04 AM, Vidya .H.K wrote:

Hi,

I am new user to galaxy. I have installed galaxy on the Linux local
server
for ChIP-seq analysis. While running MACS, an error is flagged
   An error occurred running this job: /bin/sh: macs: not found .
I have set the path for macs in /bin. But still the error persists. It
would be great if any one help me resolve this problem.



Hi Vidya

Is macs executable for the galaxy user (ie the user the galaxy server is
running as) ?

Regards, Hans


Thanks in advance.


Regards
vidya



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Regards
H.K.VIDYA
PGDB-10-10-33
-
Institute of Bioinformatics and Applied Biotechnology, Bangalore


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Re: [galaxy-dev] importing large files into local instance

[Hans-Rudolf Hotz]

Hi

Have you looked into using Data Libraries, see:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

you get access to the data without duplication.


Regards, Hans

On 01/17/2012 12:35 AM, Joshua Gross wrote:

Hello all--

We have set up a local version of Galaxy on our own server. On the same
computer, we have a couple ~27 GB fastq files we want to use in Galaxy,
but we have not figured out how to import them. Since they are on the
same HDD, we imagine that there is a way to simply copy them into a
folder or something.

Is there a simple way to import these files? We have been unable to
locate anything in the documentation that directly addresses this issue.

Thanks a lot for your time!

Josh Gross


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[galaxy-dev] changeset inconsistency

[Hans-Rudolf Hotz]

Hi

I am in the process of upgrading all our Galaxy servers to the current 
changeset (b258de1e6cea, Nov. 18) and I have noticed an inconsistency:


If I upgrade one of our old servers (which was on 720455407d1c, June 
23) with 'hg pull -u -r b258de1e6cea' I get the following:



haruhotz@silicon: hg heads
changeset:   6297:b258de1e6cea
tag: tip
user:jeremy goecks jeremy.goe...@emory.edu
date:Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

haruhotz@silicon:



If I create a new installation with
'hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist' I get the following:



haruhotz@silicon: hg heads
changeset:   6298:b258de1e6cea
tag: tip
user:jeremy goecks jeremy.goe...@emory.edu
date:Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

changeset:   5832:70b8039a2eef
branch:  feature/ws
parent:  5826:6206a27bd2ae
user:Nate Coraor n...@bx.psu.edu
date:Wed Jul 27 10:48:03 2011 -0400
summary: Closed the feature/ws branch, changes from this branch were 
merged in 5827:f3a1086fac91.


haruhotz@silicon:



I am not worry about the merged branched, I am just a little bit 
surprised about the differences:


6298:b258de1e6cea versus 6297:b258de1e6cea


Can anybody with more mercurial experience enlighten me what went wrong? 
and even better tell me that there is nothing to worry about...



Regards, Hans



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Re: [galaxy-dev] problems with location of filter bar in trackster

[Hans-Rudolf Hotz]

Hi Jeremy



A couple questions:

(a) What browser/OS are you using when seeing this problem?


chrome and firefox on Linux as well as firefox on Mac (10.5.8)



(b) Can you replicate this behavior on our public server?


it works fine on the public server



A couple notes: depending on your Web server setup, it may be necessary

 to use the packed Trackster script rather than the full one.

what do you mean by packed Trackster script

 Also, we're planning to release a new distribution in the next couple
 days, so it may be worthwhile to put off debugging Trackster until
 then because there have been quite a few changes to Trackster since
 the last release and these may solve your issues.

I am aware of the fact, that there will be an imminent release of a new 
distribution. However, I have reserved this week to do the upgrades in 
order to fit with in with other obligations I have



Regards, Hans



Thanks,
J.

On Jan 18, 2012, at 9:19 AM, Hans-Rudolf Hotz wrote:


Hi

I am still in the process of upgrading all our Galaxy servers to the current changeset 
(b258de1e6cea, Nov. 18) and now I am running into troubles with the 
visualization:


Depending on the location of my mouse, the filter bar and the other extra 
buttons jump between two positions, which makes it impossible to use, see 
Screenshot_1.png and Screenshot_2.png


I was looking for relevant code changes, which were committed after Nov. 18.  I found changeset 
856aac70b018 (Trackster: refactor action icon creation and initialization 
from Nov. 23) for ~/static/scripts/trackster.js

Adding this change fixes the problem somehow, but I lose the original icons 
(for 'set display mode', 'Hide/Show track content', etc) and the bar is now 
below the track, see Screenshot_3.png

Just using the ~/static/scripts/trackster.js from 'central' doesn't solve the 
problem either.

Are there any extra steps I can do in addition to changeset 856aac70b018 in 
order to solve this problem (except for waiting/using for the next release)


Thank you very much for your help

Hans
Screenshot_1.pngScreenshot_2.pngScreenshot_3.png___
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Re: [galaxy-dev] problems with location of filter bar in trackster

[Hans-Rudolf Hotz]

Hi Jeremy

Thank you very much for your help. I will look into your suggestions.


Regards, Hans

On 01/18/2012 10:08 PM, Jeremy Goecks wrote:


it works fine on the public server


Good, this narrows down the problem to installing the -central script on your 
instance b/c main's copy of the script is very similar to -central's.


what do you mean by packed Trackster script


All JavaScript files are compressed in size--comments/whitespace removed and 
variables renamed--to minimize their transfer time. These are available in 
/static/scripts/packed

If you have directives in your proxy server config to use the packed scripts, 
you'll want to update the packed script from -central as well.

The other thing to consider is browser caching: you may need to clear your 
browser cache to load the new Trackster script.

Good luck,
J.

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Re: [galaxy-dev] changeset inconsistency

[Hans-Rudolf Hotz]

Hi Nate

Thank you very much for your e-mail

I am still testing and working on the last distribution, hopefully going 
live this Sunday. But I will look into downloading and upgrading (one of 
our dev servers) to the new distribution next week.


Regards, Hans

On 01/19/2012 07:39 PM, Nate Coraor wrote:

Hi Hans,

We're releasing a distribution today.  If this is still the case with that 
distribution, let me know.  There were branches that weren't showing up under 
newer versions of Mercurial.  Hopefully this is all resolved in the latest.

--nate

On Jan 17, 2012, at 4:11 AM, Hans-Rudolf Hotz wrote:


Hi

I am in the process of upgrading all our Galaxy servers to the current changeset 
(b258de1e6cea, Nov. 18) and I have noticed an inconsistency:

If I upgrade one of our old servers (which was on 720455407d1c, June 23) with 
'hg pull -u -r b258de1e6cea' I get the following:


haruhotz@silicon: hg heads
changeset:   6297:b258de1e6cea
tag: tip
user:jeremy goecksjeremy.goe...@emory.edu
date:Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

haruhotz@silicon:



If I create a new installation with
'hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist' I get the following:



haruhotz@silicon: hg heads
changeset:   6298:b258de1e6cea
tag: tip
user:jeremy goecksjeremy.goe...@emory.edu
date:Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

changeset:   5832:70b8039a2eef
branch:  feature/ws
parent:  5826:6206a27bd2ae
user:Nate Coraorn...@bx.psu.edu
date:Wed Jul 27 10:48:03 2011 -0400
summary: Closed the feature/ws branch, changes from this branch were merged 
in 5827:f3a1086fac91.

haruhotz@silicon:



I am not worry about the merged branched, I am just a little bit surprised 
about the differences:

6298:b258de1e6cea versus 6297:b258de1e6cea


Can anybody with more mercurial experience enlighten me what went wrong? and 
even better tell me that there is nothing to worry about...


Regards, Hans



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Re: [galaxy-dev] software installs: PATH vs env.sh

[Hans-Rudolf Hotz]

On 01/22/2012 01:41 AM, Anthonius deBoer wrote:

All tools need to be in the path of the user running galaxy.



but can be simply added to the path by adding them to the 'run.sh' script

Regards, Hans



Regards,

Thon

Thon de Boer, Ph.D
Bioinformatics Guru

T: +1.650.799.6839 | E-mail: thondeb...@me.com

http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b

IMPORTANT NOTICE: This email message is legally privileged, confidential and is for 
the use of the individual or entity to whom it is addressed. If you have received this 
email message by error, please immediately notify us by email and delete the message. 
Thank you.

On Jan 21, 2012, at 3:50 PM, Andrew Warrenanwar...@vbi.vt.edu  wrote:


Hello,

We recently transitioned from a CloudMan instance of galaxy to our own
cluster and started having problems with calls to tools from within
other tools. For example when Tophat calls bowtie-inspect its not
finding the executable. To fix this I listed bowtie in the
requirements section of the tophat wrapper like so:

tool id=tophat name=Tophat for Illumina version=1.5.0
 descriptionFind splice junctions using RNA-seq data/description
 version_commandtophat --version/version_command
 requirements
 requirement type=packagetophat/requirement
 requirement type='package'bowtie/requirement
 requirement type=packagesamtools/requirement
 /requirements

Now I am wondering, is it generally expected that all tools used by
galaxy will have their executables on the user galaxy's PATH? Is the
above a good solution? Or is there something else likely amiss with
our galaxy setup? I think we recently pulled updates for some major
tool_shed release but I haven't been able to determine if any of the
tools listed above were affected by that.

Wish I were in Český Krumlov asking this question. Missed the
registration deadline...doh.

Thanks,
Andrew Warren

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Re: [galaxy-dev] (no subject)

[Hans-Rudolf Hotz]

As I wrote in my previous e-mail: Please send all follow-up with a cc 
to the mailing list (reply-all).


In order to debug you situation you need to simulate a complete 
commandline, the same Galaxy is doing.



Regards, Hans
On 01/23/2012 05:35 AM, Vidya .H.K wrote:


Hi,

Sorry for delayed reply. When I execute macs_wrapper.py on command line,
I get the following error.

python macs_wrapper.py
   File stdin, line 1
 python macs_wrapper.py

Thanks in advance






On 01/10/2012 06:31 AM, Vidya .H.K wrote:

Hi,
I think macs is exceutable with galaxy user.





what happens if you execute macs_wrapper.py on the command line?

Regards, Hans


PS: Please send all follow-up with a cc to the mailing list (reply-all).



On 01/09/2012 05:04 AM, Vidya .H.K wrote:

Hi,

I am new user to galaxy. I have installed galaxy on the Linux local
server
for ChIP-seq analysis. While running MACS, an error is flagged
An error occurred running this job: /bin/sh: macs: not found .
I have set the path for macs in /bin. But still the error persists. It
would be great if any one help me resolve this problem.



Hi Vidya

Is macs executable for the galaxy user (ie the user the galaxy server
is
running as) ?

Regards, Hans


Thanks in advance.


Regards
vidya



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Regards
H.K.VIDYA

-
Institute of Bioinformatics and Applied Biotechnology, Bangalore









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[galaxy-dev] allow administrators to impersonate other users

[Hans-Rudolf Hotz]

Hi

The recently added new function allowing administrators to impersonate 
other users is a really useful tool - thank you very much.


It works great on our development server. Unfortunately, it does not 
work on our production server which relies on external authentication 
via Apache.  Is this a common problem?   See below for the output in the 
logs, when I tried to switch from 'hansrudolf.h...@fmi.ch' to 
'tim.rol...@fmi.ch'.


Has anybody else activated this functionality (with or without success)?


Regards, Hans






172.27.28.201 - - [23/Jan/2012:13:25:11 +0200] POST /admin/impersonate 
HTTP/1.1 200 - http://galaxy.fmi.ch/admin/impersonate?webapp=galaxy; 
Mozilla/5.0 (X11; U; Linux i686; en-US) AppleWebKit/533.4 (KHTML, like 
Gecko) Chrome/5.0.375.86 Safari/533.4


galaxy.web.framework WARNING 2012-01-23 13:25:23,526 User logged in as 
'hansrudolf.h...@fmi.ch' externally, but has a cookie as 
'tim.rol...@fmi.ch' invalidating session


172.27.28.201 - - [23/Jan/2012:13:25:23 +0200] GET /root HTTP/1.1 200 
- http://galaxy.fmi.ch/admin/impersonate; Mozilla/5.0 (X11; U; Linux 
i686; en-US) AppleWebKit/533.4 (KHTML, like Gecko) Chrome/5.0.375.86 
Safari/533.4

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Re: [galaxy-dev] changeset inconsistency

[Hans-Rudolf Hotz]

Hi Nate

Yes, upgrading one of our old servers with hg pull -u -r 63bc46cc73b7 
and downloading a new clone with hg clone 
http://www.bx.psu.edu/hg/galaxy galaxy-dist, does not result in the 
same changeset number (ie '6528')


Thank you very much
Hans



On 01/20/2012 09:04 AM, Hans-Rudolf Hotz wrote:

Hi Nate

Thank you very much for your e-mail

I am still testing and working on the last distribution, hopefully going
live this Sunday. But I will look into downloading and upgrading (one of
our dev servers) to the new distribution next week.

Regards, Hans

On 01/19/2012 07:39 PM, Nate Coraor wrote:

Hi Hans,

We're releasing a distribution today. If this is still the case with
that distribution, let me know. There were branches that weren't
showing up under newer versions of Mercurial. Hopefully this is all
resolved in the latest.

--nate

On Jan 17, 2012, at 4:11 AM, Hans-Rudolf Hotz wrote:


Hi

I am in the process of upgrading all our Galaxy servers to the
current changeset (b258de1e6cea, Nov. 18) and I have noticed an
inconsistency:

If I upgrade one of our old servers (which was on 720455407d1c,
June 23) with 'hg pull -u -r b258de1e6cea' I get the following:


haruhotz@silicon: hg heads
changeset: 6297:b258de1e6cea
tag: tip
user: jeremy goecksjeremy.goe...@emory.edu
date: Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

haruhotz@silicon:



If I create a new installation with
'hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist' I get the
following:



haruhotz@silicon: hg heads
changeset: 6298:b258de1e6cea
tag: tip
user: jeremy goecksjeremy.goe...@emory.edu
date: Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

changeset: 5832:70b8039a2eef
branch: feature/ws
parent: 5826:6206a27bd2ae
user: Nate Coraorn...@bx.psu.edu
date: Wed Jul 27 10:48:03 2011 -0400
summary: Closed the feature/ws branch, changes from this branch were
merged in 5827:f3a1086fac91.

haruhotz@silicon:



I am not worry about the merged branched, I am just a little bit
surprised about the differences:

6298:b258de1e6cea versus 6297:b258de1e6cea


Can anybody with more mercurial experience enlighten me what went
wrong? and even better tell me that there is nothing to worry about...


Regards, Hans



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Re: [galaxy-dev] (no subject)

[Hans-Rudolf Hotz]

On 01/24/2012 06:19 AM, Vidya .H.K wrote:

Hi,
Actually I am not computer expert as well. I have just started to work in
this area. so I am not able to figure out how to solve this problem. I
request you to elaborate on what you meant in your previous mail.


by simulating a complete command line I meant the following:

You look how macs_wrapper.py is called by galaxy. This is written in 
the macs_wrapper.xml and then you execute the same command line.


But I just realize, you have re-submitted the same question in a 
different e-mail thread again (unfortunately, again without a subject 
line).





Thanks in advance






As I wrote in my previous e-mail: Please send all follow-up with a cc

to the mailing list (reply-all).

In order to debug you situation you need to simulate a complete
commandline, the same Galaxy is doing.
Regards, Hans
On 01/23/2012 05:35 AM, Vidya .H.K wrote:

Hi,
Sorry for delayed reply. When I execute macs_wrapper.py on command line,
I get the following error.
python macs_wrapper.py
File stdin, line 1
  python macs_wrapper.py
Thanks in advance

On 01/10/2012 06:31 AM, Vidya .H.K wrote:

Hi,
I think macs is exceutable with galaxy user.

what happens if you execute macs_wrapper.py on the command line?

Regards, Hans

PS: Please send all follow-up with a cc to the mailing list
(reply-all).

On 01/09/2012 05:04 AM, Vidya .H.K wrote:

Hi,
I am new user to galaxy. I have installed galaxy on the Linux local

server

for ChIP-seq analysis. While running MACS, an error is flagged
 An error occurred running this job: /bin/sh: macs: not found

.

I have set the path for macs in /bin. But still the error persists. It
would be great if any one help me resolve this problem.

Hi Vidya
Is macs executable for the galaxy user (ie the user the galaxy

server

is
running as) ?
Regards, Hans

Thanks in advance.
Regards
vidya
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Re: [galaxy-dev] Uploading large file in browser

[Hans-Rudolf Hotz]

On 01/24/2012 10:27 PM, Kim, Hyunsoo wrote:

Hello,

I have local instance of galaxy and wanted to modify “upload file” so
that I will be able to upload large files (  2GB).

The reason I am trying to do this in browser is that extra tools for FTP
do not really work in my environment because of all the constraints and
firewalls.

I came up with jQuery file upload tool
(http://blueimp.github.com/jQuery-File-Upload/), and the tool seems fine
if it is possible me to integrate into my galaxy instance.

My questions are:

-Is it too cumbersome to achieve this goal with external tools?

-how deep should I hit the galaxy (at the code level) to integrate this
jquery tool?

-Are there any alternatives to upload large files in browser without FTP?


as an alternative: have you looked into using Data Libraries, see:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files


Regards, Hans



Thanks,

Daniel



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Re: [galaxy-dev] Uploading large file in browser

[Hans-Rudolf Hotz]

On 01/25/2012 08:20 PM, Kim, Hyunsoo wrote:

Hi again,

I'm kind of lost here. Does Data Library allow regular users to upload files 
directly to Galaxy from their remote work station, or does it allow users to use files 
that are already exist in Galaxy?


just to clarify: regular user can copy (ie: using scp) their data to the 
galaxy server, and then use the advantages of Data Libraries, see the 
user_library_import_dir option in the 'universe_wsgi.ini' file.


Regards, Hans



My intention was to using HTML5 file uploader which chunks large file(  2GB) 
into smaller pieces so that regular users can upload large files through Galaxy's 
GUI without external FTP tool.

Thanks,
Hyunsoo

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Wednesday, January 25, 2012 4:02 AM
To: Kim, Hyunsoo
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Uploading large file in browser



On 01/24/2012 10:27 PM, Kim, Hyunsoo wrote:

Hello,

I have local instance of galaxy and wanted to modify upload file so
that I will be able to upload large files (  2GB).

The reason I am trying to do this in browser is that extra tools for
FTP do not really work in my environment because of all the
constraints and firewalls.

I came up with jQuery file upload tool
(http://blueimp.github.com/jQuery-File-Upload/), and the tool seems
fine if it is possible me to integrate into my galaxy instance.

My questions are:

-Is it too cumbersome to achieve this goal with external tools?

-how deep should I hit the galaxy (at the code level) to integrate
this jquery tool?

-Are there any alternatives to upload large files in browser without FTP?


as an alternative: have you looked into using Data Libraries, see:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files


Regards, Hans



Thanks,

Daniel



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Re: [galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel)

[Hans-Rudolf Hotz]

Hi Alex

Since you are talking about your public server, I assume you don't have 
external authentication. Hence, have you considered to turn on the 
allow_user_impersonation option?


Nice and very efficient way of cleaning up.


Regards, Hans


On 01/27/2012 10:43 PM, Bossers, Alex wrote:

Hi All,

We are finally up-and-running again with the latest dist release. The previoous 
version was ok but already quite old.

For our local public server at wur we are now encountering the awaited disk 
space issues. as had to come some daybut sooner anyway... So we have 
been cleaning up. Used the cleanusp scripts for marked as deleted files and 
such.

But two issues remain for galaxy-admin users:
1) How to really delete a user and its non (no-longer) shared files? (from the 
admin panel)
2) Is there a way to get the user disk space usage in the admin panel (or using 
some other method?)? Thereby we can contact that user to push cleaning up files.

Thanks
Alex




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Re: [galaxy-dev] changeset inconsistency

[Hans-Rudolf Hotz]

Hi Nate

Sorry, this was a typo, I meant to write:  does noW result in the 
same changeset number (ie '6528')   - so everything is fine now.



I apologize for the confusion

Hans



On 02/01/2012 07:13 PM, Nate Coraor wrote:

On Jan 23, 2012, at 8:01 AM, Hans-Rudolf Hotz wrote:


Hi Nate

Yes, upgrading one of our old servers with hg pull -u -r 63bc46cc73b7 and downloading a 
new clone with hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist, does not result in 
the same changeset number (ie '6528')

Thank you very much
Hans


Hi Hans,

So with the latest dist version where the changeset number is still off, is it 
still showing 2 heads?  Is the older head still 70b8039a2eef?  What version of 
Mercurial is this?

How about the output of 'hg branches', 'hg branches -a', and 'hg branches -c'?

Thanks,
--nate





On 01/20/2012 09:04 AM, Hans-Rudolf Hotz wrote:

Hi Nate

Thank you very much for your e-mail

I am still testing and working on the last distribution, hopefully going
live this Sunday. But I will look into downloading and upgrading (one of
our dev servers) to the new distribution next week.

Regards, Hans

On 01/19/2012 07:39 PM, Nate Coraor wrote:

Hi Hans,

We're releasing a distribution today. If this is still the case with
that distribution, let me know. There were branches that weren't
showing up under newer versions of Mercurial. Hopefully this is all
resolved in the latest.

--nate

On Jan 17, 2012, at 4:11 AM, Hans-Rudolf Hotz wrote:


Hi

I am in the process of upgrading all our Galaxy servers to the
current changeset (b258de1e6cea, Nov. 18) and I have noticed an
inconsistency:

If I upgrade one of our old servers (which was on 720455407d1c,
June 23) with 'hg pull -u -r b258de1e6cea' I get the following:


haruhotz@silicon: hg heads
changeset: 6297:b258de1e6cea
tag: tip
user: jeremy goecksjeremy.goe...@emory.edu
date: Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

haruhotz@silicon:



If I create a new installation with
'hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist' I get the
following:



haruhotz@silicon: hg heads
changeset: 6298:b258de1e6cea
tag: tip
user: jeremy goecksjeremy.goe...@emory.edu
date: Thu Nov 17 15:08:49 2011 -0500
summary: Pack js scripts.

changeset: 5832:70b8039a2eef
branch: feature/ws
parent: 5826:6206a27bd2ae
user: Nate Coraorn...@bx.psu.edu
date: Wed Jul 27 10:48:03 2011 -0400
summary: Closed the feature/ws branch, changes from this branch were
merged in 5827:f3a1086fac91.

haruhotz@silicon:



I am not worry about the merged branched, I am just a little bit
surprised about the differences:

6298:b258de1e6cea versus 6297:b258de1e6cea


Can anybody with more mercurial experience enlighten me what went
wrong? and even better tell me that there is nothing to worry about...


Regards, Hans



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Re: [galaxy-dev] uploads stuck in history

[Hans-Rudolf Hotz]

Hi

I guess we see similar things: a new history item is created, it turns 
purple, stays like this apparently forever while no job id is created 
(ie I don't see the job in any of the report tools).


To be honest we ignore them, because:

a) it only (as far as I can tell) happens with big data files (we try to 
avoid this anyway by using 'Data libraries') while there is heavy load 
on the storage system


b) ...eventually, unless the user has deleted the history item, it does 
turn green and the job is listed as 'ok'.



Do you experience this problem with all files, even small ones?


Regards, Hans


On 02/22/2012 10:14 AM, Jorrit Boekel wrote:

Dear list,

I have stumbled on some strange behaviour when uploading files to galaxy
via the upload.py tool. At times, the upload seems to be stalled in
history and is never actually performed, followed by a seemingly
infinite history update (see log below). My system is Ubuntu 11.10 and
runs Python 2.7.2. I find the behaviour in both my own modified galaxy
install (based on galaxy-dist), and in a fresh clone from galaxy-central.

I have tried to upload different files, and all seem to sometimes
trigger the behaviour, but not all the time. A restart of galaxy
sometimes sorts things out. Common for the debug messages is that it
seems there is never a job id generated as in
galaxy.tools.actions.upload_common INFO 2012-02-22 10:06:36,186 tool
upload1 created job id 2.

Has anyone seen similar things or can it be a problem with my system?

cheers,
jorrit






--Debug messa:

galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request
returned None from get_history(): http://localhost:8080/
127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] GET / HTTP/1.1 200 - -
Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] GET /root/tool_menu
HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] GET /history HTTP/1.1 200 -
http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] POST /root/user_get_usage
HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] GET
/tool_runner?tool_id=upload1 HTTP/1.1 200 -
http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] POST
/tool_runner/upload_async_create HTTP/1.1 200 -
http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] GET
/tool_runner/upload_async_message HTTP/1.1 200 -
http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] GET /history HTTP/1.1 200 -
http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0
(X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] POST /root/user_get_usage
HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] GET
/tool_runner?tool_id=upload1 HTTP/1.1 200 -
http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:27 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:31 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:35 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2
127.0.0.1 - - [22/Feb/2012:09:48:39 +0200] POST
/root/history_item_updates HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) 

Re: [galaxy-dev] different number output files generated based on user parameter

[Hans-Rudolf Hotz]

Hi Victor

Have you looked at the wiki page:

http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files


Variable Static Outputs determined by parameter values is probably 
what you want



Regards, Hans


On 02/24/2012 10:16 PM, Victor Ruotti wrote:

Thank you Shaun.
That worked really good!

One final question.
What is the best way to generate output files dynamically by galaxy.
That is if the user sets a parameter, say create bam file. Then the output file 
gets generated.
If the same parameter is false or no, then galaxy does not generate this file.

We tried using the when tags and the conditional tags inside the output tags 
with no luck.
Thanks again and looking forward to your response.

Victor


On Feb 24, 2012, at 4:16 AM, SHAUN WEBB wrote:





Hi Victor,

this is how I have implemented this:

param name=sample type=text format=txt label=Sample label /

data format=tabular name=filename label=${sample}.genes-results /

Shaun




Quoting VICTOR M RUOTTI wisc-mailruo...@wisc.edu  on Thu, 23 Feb 2012 
13:06:23 -0600:


Hi Peter,Thanks for the quick feedback.
Sorry if I wasn't clear.
Yes, I asking on how to set the labels for a file so instead of
data format=tabular name=filename label=genes-results/
we can have a variable that comes from the interface set by the user so it can 
be like this?
Say the user set the name from a text box to be S
We can have S saved as $prefix, something like below.
data format=tabular name=$prefix.filename label=$prefix.genes-results/


The files then will be labeled:
S.genes-results
They still be called dataset_547.dat but labeled based on the user's input?


Victor


On 02/23/12, Peter Cock
wrote:

On Thu, Feb 23, 2012 at 5:46 PM, Victor Ruottiruo...@wisc.edu  wrote:

Hi,
I hope someone can help me on how to implement this into a wrapper.


This kind of question is normally redirected to the galaxy-dev list.


We would like to add an option so the user can set a sample name
which then be used for the prefix of the output files names.


You have no control over the file names at all - Galaxy will assign
something like database/files/000/dataset_547.dat automatically.
The user never sees the file names anyway.

Are you asking about how to control the description/caption shown
to the user in Galaxy?

Peter




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Re: [galaxy-dev] en/disable field based on the state of checkbox/radiobutton

[Hans-Rudolf Hotz]

Hi Keith

It works with dropdowns and the when tag set on the same interface 
page, see:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cwhen.3E_tag_set

Regards, Hans


On 02/29/2012 07:11 PM, Keith Sheppard wrote:

Hello, From looking at the documentation for tool config syntax and I
wasn't able to spot a way to have a field enabled or disabled based on
the state of a radio button or checkbox. Is this possible? If I missed
the documentation please point me in the right direction.

I have two use cases for this: the first is that I want the user to be
able to either select from a group of preselected values (in my case
genome lengths) or enter their own value in a numeric field; the
second is that I'd like the user to be able to select from a data file
that has been stored on our server or a data file from their history.

Thank you, Keith
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Re: [galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

[Hans-Rudolf Hotz]

Hi Leandro

Although we use 'dynamic_options' successfully in many tools, it is 
still a little mystery to me sometimes - probably due to my non-existing 
python knowledge.


Hence just double checking:

Does  [ One,1,True ],
  [ Two,2,False ],
  [ Three,3,False]
  work?


Regards, Hans

On 02/29/2012 04:44 PM, Leandro Hermida wrote:

Hello,

If you have a form with an input like this:

param name=input1 type=select dynamic_options=get_options() /

And the options dynamically generated have integers as values, e.g.
options tuples like this:

[ One, 1, 1 ],
[ Two, 2, 0 ],
[ Three, 3, 0 ]

When you try to submit the galaxy form you always get the validation
error  An invalid option was selected, please verify.

regards,
Leandro
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[galaxy-dev] problems with display at UCSC

[Hans-Rudolf Hotz]

Hi everybody


This is kind of an embarrassing question, but I am struggling to get the 
display at UCSC to work.



Finally after several years, our sysadmin agreed to change the Apache 
configuration (which handles the authentication via LDAP) according to 
the configuration provided in the wiki:

http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy


So, I thought this was a piece of cake to make the display at UCSC 
work. I changed the following (in order to prevent broken links on our 
production server, I have currently restricted it to mm7, which nobody 
is using in our institute):


in universe_wsgi.ini, I have:  'ucsc_display_sites = main'

in tool-data/shared/ucsc/ucsc_build_sites.txt, I have:
'main   http://genome.ucsc.edu/cgi-bin/hgTracks?mm7'



For history items with format: bed, database: mm7 I get the link: 
display at UCSC 'main', eg:


http://galaxy.fmi.ch/datasets/13185/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dmm7%26position%3Dchr1%3A11873-1655775%26hgt.customText%3D%25sdisplay_url=http%3A%2F%2Fgalaxy.fmi.ch%2Froot%2Fdisplay_as%3Fid%3D13185%26display_app%3Ducsc%26authz_method%3Ddisplay_at



If I click on it, I get the right UCSC page (ie: mm7 
chr1:chr1:11,873-1,655,775).

But I get the following error message on the top of the page:

Expected 200 
http://galaxy.fmi.ch/root/display_as?id=13185display_app=ucscauthz_method=display_at: 
401 Authorization Required




Our sysadmin insists this is a Galaxy error (ie wrong configuration in 
the Galaxy code), but I ran out of ideas what else would need changing 
in Galaxy to make the display work.


Is there anything else I need to adjust in addition to the two changes 
in universe_wsgi.ini and ucsc_build_sites.txt?  Or is the error (as 
I suspect) somewhere in the Apache configuration.


Thank you very much for any pointers which might get the display to work 
for us


Regards, Hans
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Re: [galaxy-dev] Welcome.html page

[Hans-Rudolf Hotz]

Hi Huayan

 I got a silly question for you. My galaxy is running now but I'd like
 to customize it.
 I've changed the welcome.html page but the galaxy mirror site is
 showing the old one. Do I need to change some other files or other
 configurations?

Are you sure the page is not cached locally?

 Also, I addlable  in tool_conf.xml file but it does not show up
 either. Is there another file I need to change too?


I assume you mean label, have you restarted your galaxy server?


I hope this helps
Regards, Hans





 Best,
 Huayan
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Re: [galaxy-dev] Welcome.html page

[Hans-Rudolf Hotz]

On 03/09/2012 01:04 AM, Huayan Gao wrote:

Dear Hans,

I emptied cache and it is not showing up the changes. I changed a computer and 
tried again. No luck.

Yes, I killed the process and restart the server, no luck.

It should be pretty straight forward but it just did not come out as I expected.

Any ideas?



first (wild) guess: you have two galaxy servers (ie galaxy directories). 
you change the file in one, but in the web browser, you are looking at a 
different installation.


so just double checking: what happens when you delete (ie re-name or 
move to a different location):


  ~/galaxy_dist/static/welcome.html
  ~/galaxy_dist/tool_conf.xml
  ~/galaxy_dist/tool_conf.xml.sample

and restart the server? the missing tool_conf.xml should cause the 
start-up to fail



Regards, Hans


Best,
Huayan


On 8 Mar, 2012, at 10:52 PM, Hans-Rudolf Hotz wrote:


Hi Huayan


I got a silly question for you. My galaxy is running now but I'd like
to customize it.
I've changed the welcome.html page but the galaxy mirror site is
showing the old one. Do I need to change some other files or other
configurations?


Are you sure the page is not cached locally?


Also, I addlable   in tool_conf.xml file but it does not show up
either. Is there another file I need to change too?



I assume you mean label, have you restarted your galaxy server?


I hope this helps
Regards, Hans






Best,
Huayan
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Re: [galaxy-dev] Help writing a tool

[Hans-Rudolf Hotz]

On 03/19/2012 10:19 PM, Peter Cock wrote:

On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnsonmjohn...@ncbi.nlm.nih.gov  wrote:

I'm writing some tools to integrate NCBI data resources with Galaxy. I have
two questions.

The first is simple. I want to write a tool for a long-running process that
is handled by some other scheduler, and that produces its own job ids. Some
web services, like BLAST, for example, receive a request, and take a while
to complete processing. The job id can be used to fetch either job status or
results from the server, depending on whether it has completed. How do you
make a Galaxy tool that polls the server, and produces an output set only
when the process is complete?


Why do you need to do anything special at all for Galaxy here? I'd just
write it as a single command line call which blocks. As far as Galaxy
will know it is just a slow tool.


Yes, Galaxy is pretty good with handling 'slow' tools (ie: you can close 
the browser, and come back next morning)


However, we have one tool where we just use Galaxy to execute a job 
which manipulates data outside of the Galaxy data directory. We do 
something similar to what you have asked for initially:


We have a perl wrapper, which first submits the job using IPC::Open3, 
followed by a 'while' loop checking the status of the job and finally 
produces a 'log' file which ends up as the new galaxy history item.



Regards, Hans



The second question is, besides this mailing list, and the Galaxy wiki, is
there are good online video or text resource that explains the Galaxy
architecture and how to use it? The docs are good as far as they go, but
most of what's in thecommand  scripts in the tool files isn't documented.


There are quite a few Galaxy videos... not sure if there are any aimed
at potential developers. Are you asking about the Cheetah template
language used inside the XML for thecommand  which is almost
a scripting language in itself, or the actual wrapper scripts used in
some tools (which can be written in Python, Perl, etc)?

Peter
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Re: [galaxy-dev] reload a tool's configuration from command line

[Hans-Rudolf Hotz]

Hi Jan

This is brilliant - it is always the simple solutions you overlook - 
thank you very much!


May I just add a modified version, in case you use external 
authentication. There is no point to create a cookie, since you need to 
provide userid (not the e-mail) and password each time. So a simple line 
using the '-u' option will do:


curl --silent --data-ascii tool_id=my_toolreload_tool_button=Reload 
-u userid: http://mygalaxy.ch/admin/reload_tool



Thanks again, Hans



On 03/27/2012 11:27 AM, Haarst, Jan van wrote:

I just did a test, and this works :

First login, so you get your login cookie :

curl --cookie-jar galaxy_cookie.txt --data-ascii 
'email=jan.vanhaarst%40wur.nlwebapp=galaxypassword=geheimlogin_button=Login' 
http://dev1.ab.wurnet.nl:8086/user/login

Then use that cookie to login, and reload your tool:

curl --silent --cookie galaxy_cookie.txt --data-ascii 
tool_id=sffinforeload_tool_button=Reload 
http://dev1.ab.wurnet.nl:8086/admin/reload_tool | grep donemessage

If all went well, you get this back :

 div class=donemessageReloaded the tool:br/bname:/b  sffinfobr/bid:/b  
sffinfobr/bversion:/b  1/div

HTH,

Jan


-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-
boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: maandag 26 maart 2012 17:22
To: Tim-Christoph Roloff
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] reload a tool's configuration from command line

On Mar 22, 2012, at 11:28 AM, Tim-Christoph Roloff wrote:


Hello,

I was wondering if there is a way to trigger the reload of a tool's 
configuration from

command line.

We are using a tool that loads .xml files from tool-data. The .xml files get 
modified

by a script ran by cron frequently. Right now we reload the tool config via the 
admin
interface but ideally we could integrate the reload in the cron job.


Best regards

Tim


Hi Tim,

A few people have done it by creating a script that acts as a web client and 
performs
the function via the web interface.  There's no direct way to do it from the 
command
line without restarting the server, unfortunately.

--nate






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Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance

[Hans-Rudolf Hotz]

Hi Robert

Have you looked at the Download or Export option? - you get this 
option, when you click on the triangle next to the names of you workflows.



Regards, Hans

On 03/27/2012 08:36 PM, Robert Chase wrote:

Hello,

We are going to migrate to a new instance of the galaxy server. Our
current instance contains a number of workflows and other data that we
would like to have available on the new server. Is there a way to backup
the workflows and then reload them on the new server?

Regards,
-Robert Paul Chase
Channing Lab


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Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance

[Hans-Rudolf Hotz]

Hi Rob

I don't know what exactly you mean by new server. Assuming you are 
just talking about different hardware:


Have you considered moving 'everything' to the new server? ie copying 
the Galaxy directory tree (especially make sure you copy ~/database/ ) 
and connect to the same PostgreSQL (or MySQL) database.


If you want, I can give you more details how we successfully changed the 
hardware of our server last year



Regards, Hans



On 03/28/2012 03:31 PM, Robert Chase wrote:

Thank you that could be very helpful to our users if we can't download
them all as one big batch. I was hoping to be able to do something to
save the users the headache of having to export and upload their
workflows to the new server.

Regards,
-Rob

On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:

Hi Robert

Have you looked at the Download or Export option? - you get this
option, when you click on the triangle next to the names of you
workflows.


Regards, Hans


On 03/27/2012 08:36 PM, Robert Chase wrote:

Hello,

We are going to migrate to a new instance of the galaxy server. Our
current instance contains a number of workflows and other data
that we
would like to have available on the new server. Is there a way
to backup
the workflows and then reload them on the new server?

Regards,
-Robert Paul Chase
Channing Lab


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Re: [galaxy-dev] is there a simple way to access an arbitrary dataset's absolute path?

[Hans-Rudolf Hotz]

Hi Gus


Have a look at Shantanu's email from last October:

http://dev.list.galaxyproject.org/displaying-dataset-paths-in-the-UI-td4142007.html



It works very well for us.

Regards, Hans



On 04/05/2012 08:46 PM, W. Augustine Dunn III wrote:

Hello all:

There are times when I want to explore data produced inside my local
galaxy site without using galaxy tools. For example, I may want to run a
custom script or even just a grep type function from the command line on
a couple CuffDiff output files to get an idea of whats inside.

This requires a way to get the absolute path to that dataset as it lives
in galaxy's internal structure. The only way that I have found to do
this is to place this dataset in the shared_data/data_libraries and then
view this dataset's info as admin. This is not practical for the types
of things I want to do (simple one-off old-school command line
investigations on arbitrary files).

Is there a way for me to add this info to the standard view info page
format of datasets so that I can do this sort of thing easily? Mind you,
I am not planning to alter the data in galaxy, just look at it and
sometimes dump a summary table to a folder outside of galaxy's domain.

Thanks,

Gus

--
In science, fact can only mean confirmed to such a degree that it
would be perverse to withhold provisional assent. I suppose that apples
might start to rise tomorrow, but the possibility does not merit equal
time in physics classrooms.
/-Stephen Jay Gould/



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[galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

[Hans-Rudolf Hotz]

Hi

We are in the process of migrating our Galaxy servers to the current 
March 12, 2012 release ('6799:40f1816d6857').


We have encountered two issues, which I guess are related:


If I restart the server, I get:


 galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database 
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407 
MySQL_python egg successfully loaded for mysql dialect

Traceback (most recent call last):
  File //galaxy_dist/lib/galaxy/web/buildapp.py, line 82, in 
app_factory

app = UniverseApplication( global_conf = global_conf, **kwargs )
  File //galaxy_dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options )
  File //galaxy_dist/lib/galaxy/tool_shed/migrate/check.py, line 
42, in verify_tools

db_schema = schema.ControlledSchema( engine, migrate_repository )
  File 
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py, 
line 24, in __init__

self._load()
  File 
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py, 
line 42, in _load

data = list(result)[0]
IndexError: list index out of range



I can 'temporary' fix this by commenting-out line 36 and 37 in 
~/lib/galaxy/app.py


36#from galaxy.tool_shed.migrate.check import verify_tools
37#verify_tools( self, db_url, kwargs.get( 'global_conf', {} 
).get( '__file__', None ), self.config.database_engine_options )



...well, I don't like this fix, and I wonder if there is a better one?



I have a suspicion, that this is related to problems I encountered 
during the database schema upgrade to version 93 for our MySQL database:


at step 90to91 and 91to92 I get the following:


90 - 91...

Migration script to create the tool_version and tool_version_association 
tables and drop the tool_id_guid_map table.


0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating 
tool_version table failed: (OperationalError) (1050, Table 
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid 
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, 
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255), 
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN 
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating 
tool_version table failed: (OperationalError) (1050, Table 
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid 
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, 
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255), 
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN 
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating 
tool_version_association table failed: (OperationalError) (1050, Table 
'tool_version_association' already exists) u'\nCREATE TABLE 
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, 
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, 
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version 
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating 
tool_version_association table failed: (OperationalError) (1050, Table 
'tool_version_association' already exists) u'\nCREATE TABLE 
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, 
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, 
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version 
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()

Added 0 rows to the new tool_version table.
done
91 - 92...

Migration script to create the migrate_tools table.

0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating 
migrate_tools table failed: (OperationalError) (1050, Table 
'migrate_tools' already exists) u'\nCREATE TABLE migrate_tools 
(\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion 
INTEGER\n)\n\n' ()
0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating 
migrate_tools table failed: (OperationalError) (1050, Table 
'migrate_tools' already exists) u'\nCREATE TABLE migrate_tools 
(\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion 
INTEGER\n)\n\n' ()

done


the bizarre thing is, all three tables: 'migrate_tools', 
'tool_version_association','tool_version' are present.well, this 
explains the error: 'OperationalError 1050, Table 'migrate_tools' 
already exists 'but why were the commands executed a second and 
third time?  - what happened during the first execution?



I can execute the three create statements without problems in a dummy 
database on the same MySQl server (Server version: 

Re: [galaxy-dev] dynamic_options

[Hans-Rudolf Hotz]

Hi Deepthi


what do you want to use the 'dynamic_options' for?


the file provided in the code tag is a pyhton script, but remember the 
'code tag' is deprecated see:


http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccode.3E_tag_set



Regards, Hans

On 04/21/2012 12:48 AM, Unknown wrote:

Hi all,

Is there any help available which describes about the usage of
dynamic_options?

Is thecode  file should be a python executable or can we use perl?

Thanks and regards,
Deepthi

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Re: [galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

[Hans-Rudolf Hotz]

Hi everybody

I usually don't like people sending the same e-mail several times, so I 
apologize for just doing this, since nobody has replied to last week's 
email so far.


Although, we do not encounter any problems at the moment, I fear we will 
run into problems at a later stage (ie at the next code update). This is 
our production server.


Thank you very much for any help

Regards, Hans




On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:

Hi

We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').

We have encountered two issues, which I guess are related:


If I restart the server, I get:


galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
File //galaxy_dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File //galaxy_dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File //galaxy_dist/lib/galaxy/tool_shed/migrate/check.py, line 42,
in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 24, in __init__
self._load()
File
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range



I can 'temporary' fix this by commenting-out line 36 and 37 in
~/lib/galaxy/app.py

36# from galaxy.tool_shed.migrate.check import verify_tools
37# verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )


...well, I don't like this fix, and I wonder if there is a better one?



I have a suspicion, that this is related to problems I encountered
during the database schema upgrade to version 93 for our MySQL database:

at step 90to91 and 91to92 I get the following:


90 - 91...

Migration script to create the tool_version and tool_version_association
tables and drop the tool_id_guid_map table.

0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
(id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
(id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
tool_version_association table failed: (OperationalError) (1050, Table
'tool_version_association' already exists) u'\nCREATE TABLE
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
tool_version_association table failed: (OperationalError) (1050, Table
'tool_version_association' already exists) u'\nCREATE TABLE
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
Added 0 rows to the new tool_version table.
done
91 - 92...

Migration script to create the migrate_tools table.

0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating
migrate_tools table failed: (OperationalError) (1050, Table
'migrate_tools' already exists) u'\nCREATE TABLE migrate_tools
(\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion
INTEGER\n)\n\n' ()
0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating
migrate_tools table failed: (OperationalError) (1050, Table
'migrate_tools' already exists) u'\nCREATE TABLE migrate_tools
(\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion
INTEGER\n)\n\n' ()
done


the bizarre thing is, all three tables: 'migrate_tools',
'tool_version_association','tool_version' are present

Re: [galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

[Hans-Rudolf Hotz]

Hi Greg


I was hoping to avoid thisI will let you know the outcome.


On a related note: are there any plans to migrate all MySQL users to 
postgres? It is probably easier in the longterm.maybe a topic we can 
discuss in Chicago.


Thank you very much for your reply

Regards, Hans



On 04/24/2012 04:32 PM, Greg Von Kuster wrote:

Hello Hans,

I've stayed out of this one due to your use of mysql which I cannot personally 
support as I restrict my environment to sqlite and postgres.  However, assuming 
this is not a problem restricted to mysql, can you try the following from your 
Galaxy installation directory (you should backup your database before 
attempting this)?

$sh manage_db.sh downgrade 90

After this,
$sh manage_db.sh upgrade

Greg Von Kuster

On Apr 24, 2012, at 10:09 AM, Hans-Rudolf Hotz wrote:


Hi everybody

I usually don't like people sending the same e-mail several times, so I 
apologize for just doing this, since nobody has replied to last week's email so 
far.

Although, we do not encounter any problems at the moment, I fear we will run 
into problems at a later stage (ie at the next code update). This is our 
production server.

Thank you very much for any help

Regards, Hans




On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:

Hi

We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').

We have encountered two issues, which I guess are related:


If I restart the server, I get:


galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
File //galaxy_dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File //galaxy_dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File //galaxy_dist/lib/galaxy/tool_shed/migrate/check.py, line 42,
in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 24, in __init__
self._load()
File
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range



I can 'temporary' fix this by commenting-out line 36 and 37 in
~/lib/galaxy/app.py

36# from galaxy.tool_shed.migrate.check import verify_tools
37# verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )


...well, I don't like this fix, and I wonder if there is a better one?



I have a suspicion, that this is related to problems I encountered
during the database schema upgrade to version 93 for our MySQL database:

at step 90to91 and 91to92 I get the following:


90 -  91...

Migration script to create the tool_version and tool_version_association
tables and drop the tool_id_guid_map table.

0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
(id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
(id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
tool_version_association table failed: (OperationalError) (1050, Table
'tool_version_association' already exists) u'\nCREATE TABLE
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
tool_version_association table failed: (OperationalError) (1050, Table
'tool_version_association' already exists) u'\nCREATE TABLE
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
(id), \n\t FOREIGN KEY(parent_id) REFERENCES

Re: [galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

[Hans-Rudolf Hotz]

Hi Leandro

Thank you very much for your e-mail. Indeed, the 'migrate_tools' table 
is empty:



mysql select * from galaxy_xenon1.migrate_version;
+---+--+-+
| repository_id | repository_path  | version |
+---+--+-+
| Galaxy| lib/galaxy/model/migrate |  93 |
+---+--+-+
1 row in set (0.02 sec)

mysql select * from galaxy_xenon1.migrate_tools;
Empty set (0.05 sec)

mysql


but I guess, the table itself is correct?

mysql describe galaxy_xenon1.migrate_tools;
+-+--+--+-+-+---+
| Field   | Type | Null | Key | Default | Extra |
+-+--+--+-+-+---+
| repository_id   | varchar(255) | YES  | | NULL|   |
| repository_path | text | YES  | | NULL|   |
| version | int(11)  | YES  | | NULL|   |
+-+--+--+-+-+---+
3 rows in set (0.00 sec)

mysql


tomorrow, I will try adding the missing line manually


Thanks, Hans


On 04/24/2012 05:46 PM, Leandro Hermida wrote:

Dear Hans,


//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range


This error is because SQLAlchemy cannot load the controlled schema
version info from the DB, the result is empty, so I think its trying
to load the migrate_version and migrate_tools tables.  Make sure the
tables look like this hopefully they have each one row of data like
this:

mysql  select * from migrate_version;
+---+--+-+
| repository_id | repository_path  | version |
+---+--+-+
| Galaxy| lib/galaxy/model/migrate |  93 |
+---+--+-+
1 row in set (0.01 sec)

mysql  select * from migrate_tools;
+---+--+-+
| repository_id | repository_path  | version |
+---+--+-+
| GalaxyTools   | lib/galaxy/tool_shed/migrate |   1 |
+---+--+-+
1 row in set (0.01 sec)

hth,
Leandro

On Tue, Apr 24, 2012 at 4:09 PM, Hans-Rudolf Hotzh...@fmi.ch  wrote:

Hi everybody

I usually don't like people sending the same e-mail several times, so I
apologize for just doing this, since nobody has replied to last week's email
so far.

Although, we do not encounter any problems at the moment, I fear we will run
into problems at a later stage (ie at the next code update). This is our
production server.

Thank you very much for any help

Regards, Hans




On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:


Hi

We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').

We have encountered two issues, which I guess are related:


If I restart the server, I get:


galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
File //galaxy_dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File //galaxy_dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File //galaxy_dist/lib/galaxy/tool_shed/migrate/check.py, line 42,
in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File

//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 24, in __init__
self._load()
File

//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range



I can 'temporary' fix this by commenting-out line 36 and 37 in
~/lib/galaxy/app.py

36# from galaxy.tool_shed.migrate.check import verify_tools
37# verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )


...well, I don't like this fix, and I wonder if there is a better one?



I have a suspicion, that this is related to problems I encountered
during the database schema upgrade to version 93 for our MySQL database:

at step 90to91 and 91to92 I get the following:


90 -  91...

Migration script to create the tool_version and tool_version_association
tables and drop the tool_id_guid_map table.

0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n

Re: [galaxy-dev] More meaningful dataset names/easier method of identifying?

[Hans-Rudolf Hotz]

Hi Josh

Are you running the additional reports web site?
see:  'run_reports.sh' and 'reports_wsgi.ini'

We use this extra web site a lot for debugging. It helps tracking what 
an individual user is doing - kind of 'big brother is watching you'



Regards, Hans

On 04/24/2012 10:51 PM, Dannon Baker wrote:

In changeset 7013:dae7eefe2f71 I added the full file path to the dataset View 
Details page.  Galaxy administrators will always see this, and if you set 
expose_dataset_path to True in your universe_wsgi.ini, users will see it as well.  
Hopefully that's what you're looking for, but let me know if I've misunderstood what 
you're after and I can take another look.

-Dannon

On Apr 24, 2012, at 4:41 PM, Josh Nielsen wrote:


Hello,

For a while now with the Galaxy mirror that we have I have found on many occasions a need to identify which dataset_*.dat 
files on the file system (in the [galaxy_dist]/database/files/000/ directory) belong to which user, and even 
for the same user to distinguish between their various datasets. Files directly uploaded by the user will have a Galaxy 
job  dataset file name which match - like a Galaxy job name of data 18 (for example) which actually is 
reflective of the file name 'dataset_18.dat' on the file system. However any analysis on that file thereafter that produces 
another dataset does not give you a clue of the corresponding file name. For example, a Clip on data 18 run 
some time later may be called 'dataset_44.dat' on the filesystem, and a Map with Bowtie on data 18 that runs on 
the clipped 'dataset_44.dat' may produce an output file of 'dataset_53.dat'.

When debugging failed jobs, and after the user has rerun them for the umpteenth 
time, there may be dozens of identical or near-identical files to weed through, 
and the generic naming scheme is not helpful even though it is sequential (also 
not easy to keep track of/match up unless you are watching the file writes in 
the directory live). The current implementation makes sense for internal usage 
and the code that uses it, but it is difficult for a human to distinguish which 
files match the jobs in Galaxy.

It would be useful to have more meaningful dataset file names or an easier way to identify them (a record that matches 
the internal and external names) for administrative maintenance reasons so that I can delete 
files, or possibly even export those .dat files to a network share where our users can perform manual analysis on them. 
Could anyone point me to where in the code I could look to make the dataset names more meaningful? Or perhaps I should 
request of the Galaxy developers (as a feature) a way for the users themselves to see under the metadata 
name of their job (like Map with Bowtie on data 18) in the right side pane the *actual* corresponding 
file and location on the file system path to it (dataset_53.dat, for example). Or if not for users at least something 
for Administrators. Even a database that has four columns for the internal/filesystem dataset name, the job metadata 
name, the Galaxy job number (that the user sees), and the user that the dataset belong

!


  s to, would be helpful. A lot of our users are heavy into informatics though 
and would probably prefer that the user be able to see that information. Does 
anyone have any suggestions or thoughts about this?


Thanks,
Josh Nielsen
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Re: [galaxy-dev] One tool ,multiple set of outputs

[Hans-Rudolf Hotz]

Hi Deepthi

Have a look at:

http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20

section: 'Variable Static Outputs determined by parameter values'


Regards, Hans


On 04/24/2012 09:29 PM, Unknown wrote:

Hi all,

Can I implement a tool which run 2 different algorithms and providing different 
set of output?

Eg:Suppose I am having a tool named mytool which is running 2 different 
programs for 2 different conditions. Output of first program is a text file and 
fasta file and output of second program is a text file only.  The tool should 
produce either the outputset1 or outputset2 according to the conditions.

Can we use any kind of filter in theoutputs  tag?

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Re: [galaxy-dev] Creating a galaxy tool in R - You must not use 8-bit bytestrings

[Hans-Rudolf Hotz]

Hi Dan


There seems to be several issues connected with each other or not, I 
don't know.



- Let's start with the 'curiosity': Do you get this problem with any
  tool? Does it also happen with a 'simple' (ie not using R) tool you
  add?

- When you execute your R script on the command line, are you running
  it as the same user as Galaxy executes the job?


- we execute R scripts the following way:

 commandRscript --vanilla /full path to script/script.R -n $name
 -i $infile -o $outfile/command

  and in the R script we use the library 'getopt'



I hope this get's you a little bit further.


Regards, Hans




On 04/24/2012 11:56 PM, Dan Tenenbaum wrote:

Apologies for originally posting this to galaxy-user; now I realize it
belongs here.

Hello,

I'm a galaxy newbie and running into several issues trying to adapt an
R script to be a galaxy tool.

I'm looking at the XY plotting tool for guidance
(tools/plot/xy_plot.xml), but I decided not to embed my script in XML,
but instead have it in a separate script file, that way I can still
run it from the command line and make sure it works as I make
incremental changes. (So my script starts with args-
commandArgs(TRUE)). Also, if it doesn't work, this suggests to me that
there is a problem with my galaxy configuration.

First, I tried using the r_wrapper.sh script that comes with the XY
plotting tool,  but it threw away my arguments:

An error occurred running this job: ARGUMENT
'/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_4.dat'
__ignored__

ARGUMENT '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_3.dat'
__ignored__

ARGUMENT 'Fly' __ignored__

ARGUMENT 'Tagwise' __ignored__

etc.

So then I tried just switching to Rscript:

   command interpreter=bashRscript RNASeq.R $countsTsv $designTsv
$organism $dispersion $minimumCountsPerMillion
$minimumSamplesPerTranscript $out_file1 $out_file2/command

(My script produces as output a csv file and a pdf file. The final two
arguments I'm passing are the names of those files.)

But then I get an error that Rscript can't be found.

So I wrote a little wrapper script, Rscript_wrapper.sh:

#!/bin/sh

Rscript $*

And called that:
   command interpreter=bashRscript_wrapper.sh RNASeq.R $countsTsv
$designTsv $organism $dispersion $minimumCountsPerMillion
$minimumSamplesPerTranscript $out_file1 $out_file2/command

Then I got an error that RNASeq.R could not be found.

So then I added the absolute path to my R script to thecommand  tag.
This seemed to work (that is, it got me further, to the next error),
but I'm not sure why I had to do this; in all the other tools I'm
looking at, the directory to the script to run does not have to be
specified; I assumed that the command would run in the appropriate
directory.

So now I've specified the full path to my R script:

   command interpreter=bashRscript_wrapper.sh
/Users/dtenenba/dev/galaxy-dist/tools/bioc/RNASeq.R $countsTsv
$designTsv $organism $dispersion $minimumCountsPerMillion
$minimumSamplesPerTranscript $out_file1 $out_file2/command

And I get the following long error, which includes all of the output
of my R script:

Traceback (most recent call last):
   File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/local.py,
line 133, in run_job
 job_wrapper.finish( stdout, stderr )
   File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/__init__.py,
line 725, in finish
 self.sa_session.flush()
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py,
line 127, in do
 return getattr(self.registry(), name)(*args, **kwargs)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py,
line 1356, in flush
 self._flush(objects)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py,
line 1434, in _flush
 flush_context.execute()
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py,
line 261, in execute
 UOWExecutor().execute(self, tasks)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py,
line 753, in execute
 self.execute_save_steps(trans, task)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py,
line 768, in execute_save_steps
 self.save_objects(trans, task)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py,
line 759, in save_objects
 task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py,
line 1413, in _save_obj
 c = connection.execute(statement.values(value_params), params)
   File 
/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py,
line 824, in 

Re: [galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

[Hans-Rudolf Hotz]

Hi Leandro

brilliant!  -  adding the line manually did indeed fix the problem and I 
could remove the re-activate line 36 and 37 in  ~/lib/galaxy/app.py


Thank you very much!

now have to find out why this line was not inserted in the first place



Hans




On 04/24/2012 06:04 PM, Hans-Rudolf Hotz wrote:

Hi Leandro

Thank you very much for your e-mail. Indeed, the 'migrate_tools' table
is empty:


mysql select * from galaxy_xenon1.migrate_version;
+---+--+-+
| repository_id | repository_path | version |
+---+--+-+
| Galaxy | lib/galaxy/model/migrate | 93 |
+---+--+-+
1 row in set (0.02 sec)

mysql select * from galaxy_xenon1.migrate_tools;
Empty set (0.05 sec)

mysql


but I guess, the table itself is correct?

mysql describe galaxy_xenon1.migrate_tools;
+-+--+--+-+-+---+
| Field | Type | Null | Key | Default | Extra |
+-+--+--+-+-+---+
| repository_id | varchar(255) | YES | | NULL | |
| repository_path | text | YES | | NULL | |
| version | int(11) | YES | | NULL | |
+-+--+--+-+-+---+
3 rows in set (0.00 sec)

mysql


tomorrow, I will try adding the missing line manually


Thanks, Hans


On 04/24/2012 05:46 PM, Leandro Hermida wrote:

Dear Hans,


//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,

line 42, in _load
data = list(result)[0]
IndexError: list index out of range


This error is because SQLAlchemy cannot load the controlled schema
version info from the DB, the result is empty, so I think its trying
to load the migrate_version and migrate_tools tables. Make sure the
tables look like this hopefully they have each one row of data like
this:

mysql select * from migrate_version;
+---+--+-+
| repository_id | repository_path | version |
+---+--+-+
| Galaxy | lib/galaxy/model/migrate | 93 |
+---+--+-+
1 row in set (0.01 sec)

mysql select * from migrate_tools;
+---+--+-+
| repository_id | repository_path | version |
+---+--+-+
| GalaxyTools | lib/galaxy/tool_shed/migrate | 1 |
+---+--+-+
1 row in set (0.01 sec)

hth,
Leandro

On Tue, Apr 24, 2012 at 4:09 PM, Hans-Rudolf Hotzh...@fmi.ch wrote:

Hi everybody

I usually don't like people sending the same e-mail several times, so I
apologize for just doing this, since nobody has replied to last
week's email
so far.

Although, we do not encounter any problems at the moment, I fear we
will run
into problems at a later stage (ie at the next code update). This is our
production server.

Thank you very much for any help

Regards, Hans




On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:


Hi

We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').

We have encountered two issues, which I guess are related:


If I restart the server, I get:


galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
File //galaxy_dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File //galaxy_dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File //galaxy_dist/lib/galaxy/tool_shed/migrate/check.py, line
42,
in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File

//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,

line 24, in __init__
self._load()
File

//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,

line 42, in _load
data = list(result)[0]
IndexError: list index out of range



I can 'temporary' fix this by commenting-out line 36 and 37 in
~/lib/galaxy/app.py

36# from galaxy.tool_shed.migrate.check import verify_tools
37# verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )


...well, I don't like this fix, and I wonder if there is a better one?



I have a suspicion, that this is related to problems I encountered
during the database schema upgrade to version 93 for our MySQL
database:

at step 90to91 and 91to92 I get the following:


90 - 91...

Migration script to create the tool_version and
tool_version_association
tables and drop the tool_id_guid_map table.

0091_add_tool_version_tables

Re: [galaxy-dev] Creating a galaxy tool in R - You must not use 8-bit bytestrings

[Hans-Rudolf Hotz]

Hi Dan



I added this to my Rscript_wrapper.sh
script and all is well.



I am happy to hear that


and don't worry about answering my own question. There are always other 
people on the list which will learn from the comments and/or find the 
solution later in the mail archive  ;)



regards, Hans
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Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

[Hans-Rudolf Hotz]

Hi Ann

I am definitively interested in any form of collaboration - thank you 
very much for bringing up this idea!


However, I also share some of the concerns which have been raised by 
others. Even in Europe, we sometimes struggle to coordinate a conference 
call with the Americas and very often the quality is so bad it is 
impossible to have a discussion. Also, looking at the success of your 
original e-mail, now imagine a conference call with more than 20 
participants...


You can call me 'old fashion' but I prefer face-to-face meetings. So I 
am looking very much forward to Chicago this summer. I am aware, due to 
costs and other reasons not everybody will be able to attend GCC.


Having regional Galaxy meetings is one solution. Together with the 
Galaxy developers, I intended to organize an European Galaxy workshop as 
part of ECCB2012 in Basel in September. Unfortunately, the ECCB 
organizers did approve our proposal. I will now organize a smaller 
(Swiss) workshop in fall which will be open to everybody. I'll keep the 
list posted as soon as it has been finalized.


Nevertheless, I hope we can create an even better community and I will 
make any effort to take part in any upcoming Galaxy conference calls.



Regards, Hans









On 04/27/2012 08:45 PM, Ann Black-Ziegelbein wrote:

Hi everyone -

Here at the University of Iowa we are working on deploying Galaxy
locally for campus wide access. I am interested in forming a community
of other institutions trying to deploy Galaxy locally and mange/operate
it on a broad level. Is anyone else? If there is enough interest,
possibly we could have a community conference call every other month to
have an open discussion on how we are all deploying galaxy,
customizations we are making, problems we are encountering, bugs, and
any add-on operations management for galaxy being developed, etc.

Would love to hear from others operating Galaxy or in process of
standing up a local deployment.

Thanks!

Ann Black-Ziegelbein
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Re: [galaxy-dev] Galaxy Admin - Browsing any user's histories?

[Hans-Rudolf Hotz]

On 05/03/2012 12:10 PM, Peter Cock wrote:

Hi all,

Is it possible for a Galaxy Admin to browse any user's history?
Sadly the Admin page on the wiki is still rather lean:
http://wiki.g2.bx.psu.edu/Admin/Interface

For instance, I've monitored a large Galaxy job on our cluster, and now
that it has finished I'd like to see the results (in this case, the error
messages) - without having to first ask the user to share their history
with me. Is that possible via the normal Galaxy Admin pages?


for cases like this, we use the additional galaxy report server. It is 
very handy to track down what went wrong (ie how did the executed 
command look like) and who was the 'culprit' (see: 'reports_wsgi.ini' )




Alternatively, is this something I could do via the impersonation
option? i.e. enable allow_user_impersonation in universe_wsgi.ini


allow_user_impersonation is great and will probably help in your 
situation as well. Unfortunately, it does not (yet) work with external 
authentication, to follow up, see:

https://bitbucket.org/galaxy/galaxy-central/issue/705/


Regards, Hans




Thanks,

Peter
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Re: [galaxy-dev] ImportError: No module named NSISSoft.NSISBase

[Hans-Rudolf Hotz]

Hi Kleo

The easiest way is to add the path information to 'run.sh', eg:

export PYTHONPATH=/data/foo/bar/python2.6/site-packages:$PYTHONPATH

(of course, you need to use a different path)

Regards, Hans

On 05/03/2012 08:29 PM, Kleo Achilleos wrote:

Dear all,

I have a local installation of Galaxy.
I need to create a new galaxy tool.
My python program runs outside Galaxy. When I call it through Galaxy it
does not find my custom libraries.
/
/
/ImportError: No module named NSISSoft.NSISBase/
/
/
/I understand it is a PYTHONPATH problem. How can I fix it?/
/
/
/Kleo Achilleos/
/MSc student at UCY, Cyprus/


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Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance

[Hans-Rudolf Hotz]

On 05/03/2012 08:29 PM, Robert Chase wrote:

Hello,

We have an existing galaxy instance that uses MySQL, has workflows and
data libraries and countless changes to the source code and tools. We
would like to save the database, workflows and data libraries but bring
all the sourcecode up to date with the standard galaxy code. Because
over 3000 of our files have been changed, we do not believe that we can
realistically run hg update and then hg merge.

We have built a test instance of galaxy that runs on a different virtual
machine. One thought is to clone it, migrate all the datasets to it and
then use the clone as the new production instance.

One specific piece of information would be very helpful. Can we just
copy the ~/data files to the test instance and have galaxy recognize
them or is there metadata stored in the database?



Hi Rob 3000

You need a copy of your MySQL database for your new test instance of 
galaxy to connect to. This should get you going initially.


Most likely, you will then stumble across a few problems:

 - you need to sync ~/galaxy_dist/tool-data/shared/

 - you need to check the data libraries: are they copies or sym-links

 - you need to decide how many of you changes to the tools you want to
   port to the new server. In an ideal world you would need all in
   order to maintain the reproducibility...this might be tricky,
   especially if you have defined your own data types. In this case a
   simple copy of the 'tools/' directory and the 'tool_conf.xml' is not
   sufficient anymore

 - an more...

Nevertheless, you said you made more than 3000 changes to code and 
tools, so I guess, you are very proficient with the inner works of 
Galaxy. Hence, I see no problem, why you should not be successful.



Regards, Hans





-Rob

On Wed, Mar 28, 2012 at 10:16 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:

Hi Rob

I don't know what exactly you mean by new server. Assuming you are
just talking about different hardware:

Have you considered moving 'everything' to the new server? ie
copying the Galaxy directory tree (especially make sure you copy
~/database/ ) and connect to the same PostgreSQL (or MySQL) database.

If you want, I can give you more details how we successfully changed
the hardware of our server last year


Regards, Hans




On 03/28/2012 03:31 PM, Robert Chase wrote:

Thank you that could be very helpful to our users if we can't
download
them all as one big batch. I was hoping to be able to do
something to
save the users the headache of having to export and upload their
workflows to the new server.

Regards,
-Rob

On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch
mailto:h...@fmi.ch mailto:h...@fmi.ch wrote:

Hi Robert

Have you looked at the Download or Export option? - you get this
option, when you click on the triangle next to the names of you
workflows.


Regards, Hans


On 03/27/2012 08:36 PM, Robert Chase wrote:

Hello,

We are going to migrate to a new instance of the galaxy server. Our
current instance contains a number of workflows and other data
that we
would like to have available on the new server. Is there a way
to backup
the workflows and then reload them on the new server?

Regards,
-Robert Paul Chase
Channing Lab


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Re: [galaxy-dev] ImportError: No module named NSISSoft.NSISBase

[Hans-Rudolf Hotz]

On 05/04/2012 04:06 PM, Kleo Achilleos wrote:

Hans, thank you for your reply.


I added the path in run.sh located in galaxy_dist

export PYTHONPATH=/usr/local/devel:$PYTHONPATH

but I still get the same error
/
/
/
/usr/local/devel/NSISSoft/NSISToolkit/NSISApps/SmplTK/load_compounds.py,
line 29, in module
from NSISSoft.NSISBase import Messengers
/
/ImportError: No module named NSISSoft.NSISBase/

Do you have any other suggestions?



well, I am not familiar with this Toolkit (and not really a python 
expert), so there might be something special about this modulebut my 
first guess: the module is simply not there.


Is it working when you execute it on the the command line (as the same 
user Galaxy is running as)?


Regards, Hans



Regards, Kleo.

2012/5/4 Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch

Hi Kleo

The easiest way is to add the path information to 'run.sh', eg:

export PYTHONPATH=/data/foo/bar/__python2.6/site-packages:$__PYTHONPATH

(of course, you need to use a different path)

Regards, Hans


On 05/03/2012 08:29 PM, Kleo Achilleos wrote:

Dear all,

I have a local installation of Galaxy.
I need to create a new galaxy tool.
My python program runs outside Galaxy. When I call it through
Galaxy it
does not find my custom libraries.
/
/
/ImportError: No module named NSISSoft.NSISBase/
/
/
/I understand it is a PYTHONPATH problem. How can I fix it?/
/
/
/Kleo Achilleos/
/MSc student at UCY, Cyprus/


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Re: [galaxy-dev] Moving Data to New Instance

[Hans-Rudolf Hotz]

On 05/15/2012 05:42 PM, Robert Chase wrote:

Hello All,

We have a large amount of data on our production server that we would
like to make available on our new test server. I tried to move data from
our production server to our test server by copying the meta-data files
and dataset files from ~/database/files to the new test server but it
didn't work. Is there a way to move the datasets en mass?


Hi Rob


At the risk of repeating myself - sorry: You need a copy of your MySQL 
database for your new test instance of galaxy to connect to.


what exactly does not work? what kind of error messages do you get?


Regards, Hans





-Rob


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Re: [galaxy-dev] Error executing tool: cannot find 'database'

[Hans-Rudolf Hotz]

Hi Marine

Could you please provide the tool definition xml file. Otherwise it is 
going to be difficult to guess, what is going wrong


Regards, Hans


On 05/30/2012 11:10 AM, Marine Rohmer wrote:

Hi everyone,

I'm trying with all my best to add an NGS tool into my local Galaxy
instance.
I've added my tool in tool_conf.xml, and made a XML file with all the
command, param etc... I think it's pretty ok, and everything is
correctly displayed on the Galaxy interface.

However, when I execute my tool, Galaxy says to me :

Error executing tool: cannot find 'database'


And in my shell, I can see :

127.0.0.1 - - [30/May/2012:10:47:01 +0200] GET
/tool_runner?tool_id=myTool HTTP/1.1 200 -
http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:12.0) Gecko/20100101 Firefox/12.0
galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while
attempting tool execution:
Traceback (most recent call last):
File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line
1345, in handle_input
_, out_data = self.execute( trans, incoming=params, history=history )
File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line
1661, in execute
return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid, history=history, **kwargs )
File
/home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py,
line 333, in execute
data.name = fill_template( output.label, context=params )
File /home/myName/work/galaxy-dist/lib/galaxy/util/template.py, line
9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py,
line 1004, in __str__
return getattr(self, mainMethName)()
File DynamicallyCompiledCheetahTemplate.py, line 83, in respond
NotFound: cannot find 'database'
127.0.0.1 - - [30/May/2012:10:47:07 +0200] POST /tool_runner/index
HTTP/1.1 200 - http://localhost:8080/tool_runner?tool_id=myTool;
Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101
Firefox/12.0

I'm a beginner in computer sciences, so I can't understand since over 1
week what's happening ... Any idea what's wrong with this ?
(I'm using Ubuntu LTS 12.04)

All help will be very very appreciated !

Thank you,

Marine


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Re: [galaxy-dev] Re : Error executing tool: cannot find 'database'

[Hans-Rudolf Hotz]

Hi Marine

In addition to Ross' comment earlier, there are a few points in the xml 
I think they are wrong or at least I would code them differently - see 
my comments in between your text below


On 05/30/2012 12:32 PM, Marine Rohmer wrote:

Hi Hans,

Here is my XML file in a simplificated version (no conditionnal
parameters) , -i -r and -k are the mandatory arguments of my tool,
written in C++:


tool id=myTool name=myTool

description the description /description

command interpreter=C++
/home/myName/work/galaxy-dist/tools/NGStools/myTool
-i=${genome_index}
-r=${input}
-k=${kmer_length}
-o=${output_name}
/command



There is no variable ${genome_index}, ${input},${output_name}. You 
defined them as: $i, $r, and $o .


Hence, I would write:

   command /home/myName/work/galaxy-dist/tools/NGStools/myTool
 -i=$i
 -r=$r
 -k=$kmer_length
 -o=$o
   /commandcd


inputs
param name=i type=select label=Genome index
option value=Human path/to/Human /option
option value=E.coli path/to/Escherichia coli /option
/param

param format=txt name=r type=data label=Source File
help=Select a file/
param format=raw name=r type=data label=Source File
help=Select a file/
param format=doc name=r type=data label=Source File
help=Select a file/
param format=fastq name=r type=data label=Source File
help=Select a file/



I would write this in one line:

param format=txt,raw,doc,fastq name=r type=data label=Source 
File help=Select a file/


Also, have you defined the 'raw' and the 'doc' format?


param name=kmer_length type=integer min=15 max=150 value=21
label=k-mer length/


param name=o type=text optional=true label=Output name/


/inputs

outputs
data format=sam name=myTool_outfile label=myTool on
${database.value_label} /
/outputs



How about:

data format=sam name=myTool_outfile label=myTool on $o /


tests
test
/test
/tests

help



/help

/tool
/tool



there is one /tool too much



Hope this helps, Hans





Regards,
Marine




*De :* Hans-Rudolf Hotz h...@fmi.ch
*À :* Marine Rohmer marine.roh...@yahoo.fr
*Cc :* galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
*Envoyé le :* Mercredi 30 mai 2012 11h42
*Objet :* Re: [galaxy-dev] Error executing tool: cannot find 'database'

Hi Marine

Could you please provide the tool definition xml file. Otherwise it is
going to be difficult to guess, what is going wrong

Regards, Hans


On 05/30/2012 11:10 AM, Marine Rohmer wrote:
  Hi everyone,
 
  I'm trying with all my best to add an NGS tool into my local Galaxy
  instance.
  I've added my tool in tool_conf.xml, and made a XML file with all the
  command, param etc... I think it's pretty ok, and everything is
  correctly displayed on the Galaxy interface.
 
  However, when I execute my tool, Galaxy says to me :
 
  Error executing tool: cannot find 'database'
 
 
  And in my shell, I can see :
 
  127.0.0.1 - - [30/May/2012:10:47:01 +0200] GET
  /tool_runner?tool_id=myTool HTTP/1.1 200 -
  http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux
  x86_64; rv:12.0) Gecko/20100101 Firefox/12.0
  galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while
  attempting tool execution:
  Traceback (most recent call last):
  File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line
  1345, in handle_input
  _, out_data = self.execute( trans, incoming=params, history=history )
  File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line
  1661, in execute
  return self.tool_action.execute( self, trans, incoming=incoming,
  set_output_hid=set_output_hid, history=history, **kwargs )
  File
  /home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py,
  line 333, in execute
  data.name = fill_template( output.label, context=params )
  File /home/myName/work/galaxy-dist/lib/galaxy/util/template.py, line
  9, in fill_template
  return str( Template( source=template_text, searchList=[context] ) )
  File
 
/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py,
  line 1004, in __str__
  return getattr(self, mainMethName)()
  File DynamicallyCompiledCheetahTemplate.py, line 83, in respond
  NotFound: cannot find 'database'
  127.0.0.1 - - [30/May/2012:10:47:07 +0200] POST /tool_runner/index
  HTTP/1.1 200 - http://localhost:8080/tool_runner?tool_id=myTool;
  Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101
  Firefox/12.0
 
  I'm a beginner in computer sciences, so I can't understand since over 1
  week what's happening ... Any idea what's wrong with this ?
  (I'm using Ubuntu LTS 12.04)
 
  All help will be very very appreciated !
 
  Thank you,
 
  Marine
 
 
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Re: [galaxy-dev] Re : Re : Error executing tool: cannot find 'database'

[Hans-Rudolf Hotz]

Hi Marine

If I use the xml file as you have posted in this e-mail, it works. ie it 
works up to the error message:


  An error occurred running this job:
   /bin/sh: /home/myName/myToolRepository/bin/myTool: not found  


I don't get the cheetah error you show. Are you sure, you are using the 
same xml file?


Regards, Hans


On 05/30/2012 06:06 PM, Marine Rohmer wrote:

Ok, when I remove interpreter = C++ from command, and keep it empty
or write interpreter = bash instead, I have no more this error
message. Galaxy says The following job has been successfully added to
the queue,and I can show its progression on the history.
Thank you Ross !

But now I have a new error message that I can't solve :
An error occurred running this job: /failure preparing job
/Details are:
Traceback (most recent call last): File
/home/myName/work/galaxy-dist/lib/galaxy/jobs/runners/local.py, line
59, in run_job job_wrapper.prepare()
File /home/myName/work/galaxy-dist/lib/galaxy/jobs/__init__.py, line
429, in prepare self.command_line = self.tool.build_command_line(
param_dict )
File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line
1971, in build_command_line command_line = fill_template( self.command,
context=param_dict )
File /home/myName/work/galaxy-dist/lib/galaxy/util/template.py, line
9, in fill_template return str( Template( source=template_text,
searchList=[context] ) )
File
/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py,
line 1004, in __str__ return getattr(self, mainMethName)() File cheetah
cheetah_DynamicallyCompiledCheetahTemplate_1338392112_91_81444.py,
line 83, in respond NotFound: cannot find 'HOME'

I've tried to put an erroneous path/to/myTool in command in order to
see if my original path is right. It indeed gives me another error
message saying An error occurred running this job: //bin/sh: 1:
path/to/myTool: not found/ , which makes sense since the path is erroneous.

I've also tried to put some erroneous data in the XML file (for example
wrong names in param) to see if it influences the error message, but I
still have the same. (that is to say : NotFound: cannot find 'HOME')

With Hans' help, my XML file is bettered that way :

tool id=mytool name=My Tool
description description /description
command  /home/myName/myToolRepository/bin/myTool
-i = $genome_index
-r = $input
-k = $kmer_length
/command

inputs
param name=genome_index type=select label=Genome index
option value=E.coli /path/to/indexEcoli /option
option value=Human path/to/indexHuman /option
/param

param format=txt, raw, doc, fastq name=input type=data
label=Source File help=Select a file/

param name=kmer_length type=integer min=15 max=150 value=21
label=k-mer length/
/inputs

outputs
data format=sam name=crac_outfile label=crac outfile /
/outputs
tests
test
/test
/tests
help
/help
/tool

Regards,
Marine


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Re: [galaxy-dev] [galaxy-user] email database

[Hans-Rudolf Hotz]

Hi Roger

Have a look at the Reserved Variables on this wiki page:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?#A.3Ccommand.3E_tag_set

I guess, his is what you are after?


Also, please use the 'galaxy-dev' mailing list (cc'ed) for questions 
regarding local installation, configuration, tool integration help, etc



regards, Hans



On 06/04/2012 11:54 AM, Roger Liu wrote:

hi im the new user at intalling my own galaxy
and i developing some of the tools
now i face a challenge
i need to call the login(now) email address form my tools
but i didnt find any API can did this
so i was wondering is there had any database store the email address
i need to identify the login user's email and return back to my tool
thanks


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Re: [galaxy-dev] disk space for local galaxy

[Hans-Rudolf Hotz]

Hi

Have you looked at the wiki pages?

http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently

and

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%20Datasets



Regards, Hans

On 06/04/2012 05:29 PM, Xu, Jianpeng wrote:

Hi,

I have installed the local galaxy. I deleted a few histories in order to
get some disk space. However, the disk space did not change after the
deletion of the histories.

Do you why ? How can I get some disk space by deleting histories ?

Thanks,





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Re: [galaxy-dev] Adding mm10 to available genomes

[Hans-Rudolf Hotz]

Hi Larry

Have you added mm10   Mouse Dec. 2011 (GRCm38/mm10) (mm10) to

 ~/galaxy_dist/tool-data/shared/ucsc/builds.txt

and restarted the server?


Regards, Hans



On 06/08/2012 06:19 PM, Larry Helseth wrote:

I'm trying to add mm10 to a Galaxy instance built using Mercurial on May
31st (using Postgres). I've added the .fa file, prepared bwa, bowtie,
samtool indexes, etc., edited all of the .loc files for individual tools
and restarted the server daemon. mm10 appears in the list of genomes
available for these tools but doesn't appear in the list of all genomes
when I try uploading a file (Get Data/Upload File from your computer) OR
when I try adding the file through the admin library interface
(Administration/Data/Manage libraries/Add datasets). I tried editing
~/galaxy-dist/scripts/loc_files/create_all_fasta_loc.py to add a line
for mm10. restarting Galaxy but that genome still doesn't appear in
the list.
Do I need to edit an entry in Postgres? When I restart Galaxy without
the daemon mode (or tail the paster.log) I see that clicking on Get
Data/Upload File is calling GET /tool_runner?tool_id=upload1 for the my
URL/root/tool_menu.
Am I supposed to upload new genomes through the Library?
screencast.g2.bx.psu.edu http://screencast.g2.bx.psu.edu is still down
so I can't watch the video tutorials about configuring custom genomes.
I'd appreciate any suggestions. Thanks in advance!
Adios,
Larry

Larry Helseth, Ph.D.

Center for Molecular Medicine

NorthShore University HealthSystem

Evanston, IL



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Re: [galaxy-dev] disk space for local galaxy

[Hans-Rudolf Hotz]

 - Please keep all replies on the list by using reply all -


check your universe_wsgi.ini file:

# Allow users to remove their datasets from disk immediately (otherwise,
# datasets will be removed after a time period specified by an 
administrator in

# the cleanup scripts run via cron)
#allow_user_dataset_purge = False


Regards, Hans


On 06/11/2012 05:08 PM, Xu, Jianpeng wrote:

Hi,

I read them and tried to work according to the instruction below on the
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently

*Active* and *Deleted* histories can be *permanently deleted *using from
the History pane Options - Saved Histories, then click on Advanced
Search, then click on status: all. Check the box for the histories to
be discarded and then click on the button Permanently delete. I do not
find the Permanently delete button. I found a button Delete and
remove datasets from disk, but I click on it and it did not work.

Do you know how to fix it ?

Actually I want to delete some histories permanently and get some disk
space.

Thanks a lot.

Jianpeng



Hi

Have you looked at the wiki pages?

http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently

and

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%20Datasets



Regards, Hans

On 06/04/2012 05:29 PM, Xu, Jianpeng wrote:

 Hi,

 I have installed the local galaxy. I deleted a few histories in order to
 get some disk space. However, the disk space did not change after the
 deletion of the histories.

 Do you why ? How can I get some disk space by deleting histories ?

 Thanks,



 

 This e-mail message (including any attachments) is for the sole use of
 the intended recipient(s) and may contain confidential and privileged
 information. If the reader of this message is not the intended
 recipient, you are hereby notified that any dissemination, distribution
 or copying of this message (including any attachments) is strictly
 prohibited.

 If you have received this message in error, please contact
 the sender by reply e-mail message and destroy all copies of the
 original message (including attachments).


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Re: [galaxy-dev] Instructions for migrating users, configuration and data to other Galaxy machine

[Hans-Rudolf Hotz]

Hi Joachim

This is roughly what we did  ~15 months ago:

1. make a copy of the MySQL DB (postgresdb in your case)

2. copy the complete galaxy directory to the new server (make sure you
   keep the path)

3. point the new galaxy server to the DB copy and start it (different
   port number)
   - due to the higher Python version, news eggs were downloaded
   - all python code was re-compiled

4. test the new server (while the old one is still in use)

5. stop the old server

6. rsync  ~/galaxy_dist/database/files/

7. point the new galaxy server to the 'live' DB and re-start it


Obviously, this is won't be a 'fresh' Galaxy install.

If you want to start from a new download of the galaxy distribution, the 
amount of work (eg: merging of configuration files) depends on the 
existing modifications you have made. If you have only a few, the 
copy/merge of the: universe_wsgi.ini and tool_conf.xml files
plus a copy of the database/ and tools/ directory might be 
sufficient...or you need to look into the tool-data/ directory, the 
datatypes_conf.xml file, etc, etcbut you can test all this while the 
new server is already running in parallel to the current server.


Regards, Hans







On 06/12/2012 01:14 PM, Joachim Jacob wrote:

Hi all,


I am looking for instructions to migrate users, configuration and data
to other Galaxy machine. I have a production Galaxy, with users,
histories, pages, data libraries, configured tool panel, running on a
postgresdb. I want to move this information to a fresh Galaxy install
(same version as production) on another machine.

Is this feasible to do without much hassle? I am thinking about a
merge/sync of configuration files and dumping and creating the
postgresdb,... Has anyone experience with this and a check list for this?

The idea is that the user should have no clue that Galaxy is on a new
machine: all data, tools, histories, etc... are there. Thanks for your
consideration.


Kind regards,
Joachim



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Re: [galaxy-dev] Giardine et al Galaxy paper (2005)

[Hans-Rudolf Hotz]

Hi Peter

Have a look at Anton's talk Introduction to Galaxy at last years GCC 
meeting: http://wiki.g2.bx.psu.edu/Events/GCC2011


The first few slides are talking about the history of Galaxy, eg:

Galaxy as a single Perl script (!)


Regards, Hans

On 06/12/2012 01:28 PM, Peter van Heusden wrote:

Hi everyone

The Galaxy system as described in Belinda Giardine et al's 2005 Genome
Research paper (Galaxy: A platform for interactive large-scale genome
analysis) appears to be radically different from the current Galaxy, at
least in its technical specification. The paper mentions a C core spoken
to by a Perl-based web user interface (referred to as the History User
Interface). The co-authors on the paper are, however, familiar names
from the current Galaxy team. Was this paper describing something in the
pre-history of current Galaxy (it sounds rather like the current History
but without workflows and of course implemented on a different platform)?

Peter
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Re: [galaxy-dev] Instructions for migrating users, configuration and data to other Galaxy machine

[Hans-Rudolf Hotz]

On 06/12/2012 04:04 PM, Joachim Jacob wrote:

Hi Hans-Rudolf,


Thank you for sharing your experience!

To summarize:
1. user information is stored in the database (histories, pages,
workflows). This info is linked to the datasets,
2. all datasets are in the '../database/files' (or the location
specified in universe_wsgi.ini) directory, and
3. all configuration files are located in the root of Galaxy.

So would it be feasible to run the postgresdb not locally, but on a
separate machine, to which I connect the freshly installed Galaxy?
Then I can also keep the datasets directory on a network share, which is
mounted to the fresh install.
[perhaps other directories can also be accessed over the network, such
as the toolshed tools directory].



No, don't share the postgresdb and the datasets. Two different galaxy 
installations accessing the same postgresdb and the datasets will cause 
troubles.


Hence, I have step 6 and 7 in my procedure, to make sure all the data 
accumulated during the test phase gets 'replaced' with all the data the 
users continue to produce on the old production server.



The configuration files is perhaps the most difficult part. these have
to be merged. But perhaps I could use mercurial for this? Seems a
powerful way to do this.


Yes, to some extend, see the .hgignore file


Regards, Hans




Joachim.

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib



On 06/12/2012 02:29 PM, Hans-Rudolf Hotz wrote:

Hi Joachim

This is roughly what we did ~15 months ago:

1. make a copy of the MySQL DB (postgresdb in your case)

2. copy the complete galaxy directory to the new server (make sure you
keep the path)

3. point the new galaxy server to the DB copy and start it (different
port number)
- due to the higher Python version, news eggs were downloaded
- all python code was re-compiled

4. test the new server (while the old one is still in use)

5. stop the old server

6. rsync ~/galaxy_dist/database/files/

7. point the new galaxy server to the 'live' DB and re-start it


Obviously, this is won't be a 'fresh' Galaxy install.

If you want to start from a new download of the galaxy distribution,
the amount of work (eg: merging of configuration files) depends on the
existing modifications you have made. If you have only a few, the
copy/merge of the: universe_wsgi.ini and tool_conf.xml files
plus a copy of the database/ and tools/ directory might be
sufficient...or you need to look into the tool-data/ directory, the
datatypes_conf.xml file, etc, etcbut you can test all this while
the new server is already running in parallel to the current server.

Regards, Hans







On 06/12/2012 01:14 PM, Joachim Jacob wrote:

Hi all,


I am looking for instructions to migrate users, configuration and data
to other Galaxy machine. I have a production Galaxy, with users,
histories, pages, data libraries, configured tool panel, running on a
postgresdb. I want to move this information to a fresh Galaxy install
(same version as production) on another machine.

Is this feasible to do without much hassle? I am thinking about a
merge/sync of configuration files and dumping and creating the
postgresdb,... Has anyone experience with this and a check list for
this?

The idea is that the user should have no clue that Galaxy is on a new
machine: all data, tools, histories, etc... are there. Thanks for your
consideration.


Kind regards,
Joachim




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Re: [galaxy-dev] Query Fastq files for particular sequence elements

[Hans-Rudolf Hotz]

Hi Jane

I recommend mapping the data again yourself

Alternatively, you might wanna play with 'grep' (if you have the Galaxy 
Unix tools installed in your Galaxy server), or use the tool 'Select 
lines that match an expression'. I would do a Fastq to Tab on your data 
first. Or you can try the emboss tool 'fuzznuc' on the Fasta version of 
you data.


...but assuming you are talking about 'big' fastq files, mapping the 
data again yourself is most likely the way to go.


Regards, Hans



On 06/14/2012 07:12 PM, Jane Dorweiler wrote:

Greetings all,
I've been trying to find a way to query fastq files for particular
sequence elements. Our data was mapped using BWA by our collaborator,
and repetitive elements 'ignored', but we are now interested in
determining whether a couple specific repetitive elements of interest
are differentially represented in the raw read files. Are there any
tools that anyone has developed to do anything like this -- and that
perhaps I'm simply missing as I explore the available tools?
In the short term, I've written a very crude python script to begin
exploring the question, but I'm sure there has to be a much better way.
If there are no such tools available, I'm hopeful that someone might
have some helpful suggestions, or that perhaps it could be explored
during the upcoming conference /or training day in July.
Thanks and Best Regards, Jane
--
Jane E. Dorweiler, PhD



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Re: [galaxy-dev] No module named galaxy !!

[Hans-Rudolf Hotz]

On 06/19/2012 07:11 PM, Chebbi Mohamed Amine wrote:

Hi Galaxy team !
I'am trying to remove userless histories from my galaxy database as
mentoned in this link (
by using the command above :
python cleanup_datasets.py universe_wsgi.ini -d 60 -1
However I get an error message like this :

File cleanup_datasets.py, line 13, in module
from galaxy import eggs
ImportError: No module named galaxy



looks like you are calling the script from:

 ~/galaxy_dist/scripts/cleanup_datasets/


try calling it with:

python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 
60 -1


from:  ~/galaxy_dist/



Regards, Hans



Although I set cleanup_job = never in my Galaxy config and check the PBS
script like mentioned in the mailing list discussions as above , i have
always the same problem of galaxy module :

GALAXY_LIB=/path/to/galaxy-dist/lib
if [ $GALAXY_LIB != None ]; then
if [ -n $PYTHONPATH ]; then
export PYTHONPATH=$GALAXY_LIB:$PYTHONPATH
else
export PYTHONPATH=$GALAXY_LIB
fi
fi

Could someone help me please !

Thanks
Amine


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Re: [galaxy-dev] (no subject)

[Hans-Rudolf Hotz]

Hi Carlos

See: galaxy_dist/lib/galaxy/util/__init__.py

for characters that are allowed but need to be escaped


Regards, Hans



On 06/28/2012 03:14 PM, Carlos Reyes wrote:

Hello,

I have never used this support route before however I have a question
about a Galaxy wrapper that I made for a python tool. I have a text
input box connected to a $command_line_spot in an attempt to run a
string such as IN[4]=='gene' on the command line (quotations included)
through text box input. When I put IN[4]=='gene' directly in the
command line it runs fine, however when I put it through my text box it
puts the string on the command line
as __dq__IN__ob__4__cb__==__sq__gene__sqdq__ IN[4]=='gene' instead
of just IN[4]=='gene'. Sorry if this email makes no sense whatsoever,
it is very out of context but I thought I'd ask.

Note: I am running the latest release of galaxy which I pulled from
mercurial.

Thanks,
Carlos

The information in this email, including attachments, may be
confidential and is intended solely for the addressee(s). If you believe
you received this email by mistake, please notify the sender by return
email as soon as possible.



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Re: [galaxy-dev] error running workflow

[Hans-Rudolf Hotz]

Hi Jaap

are you using 'SQLite', if so, I recommend to switch to 'PostgreSQL', 
see: 
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server/#Switching_to_a_database_server



Regards, Hans



On 07/02/2012 02:26 PM, j.w.f.van_der_heij...@lumc.nl wrote:



Hi all,

I have added some tools to my local install of Galaxy. To get to my
final results I have to do a lot of steps.  When I try to run every step
separately it turns out to work out fine. But when I try to run all
steps at once with a workflow I get the following error message.

|OperationalError: (OperationalError) database is locked u'UPDATE
dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2012-07-02
11:34:48.135419', 'queued', 529]

I have noticed that the processes eat a lot of my computer resources.
Other than that I have no clue what the problem could be.

Any tips are appreciated.

Kind regards,
Jaap van der Heijden
|


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Re: [galaxy-dev] Emailing to all our Galaxy users

[Hans-Rudolf Hotz]

Hi Joachim

Go to Admin Menu - Security - Manage users. This will give you a list 
of all users.


Alternatively, use the reports tool: Users - Date of last login and 
select 0 days


Hope this helps,
Regards, Hans

On 08/06/2012 10:14 AM, Joachim Jacob wrote:

Dear devs,

How can I extract a list of the email addresses of all users of our Galaxy?

Cheers,
Joachim


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Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

[Hans-Rudolf Hotz]

maybe you need to include username, password and host?

database_connection = 
mysql://username:password@host/database?unix_socket=/var/run/mysqld/mysqld.sock


Regards, Hans


On 08/07/2012 03:19 AM, Kenneth Auerbach wrote:

Hello,

Galaxy runs fine 'out of the box' with the default universe_wsgi.ini
initialization file. But when I change the database_connection
statement to connect to my MySql database, I get the errors below. Can
you please tell what the problem is?  Thanks!

-Wolf.


Modification to universe_wsgi.ini file:

#database_connection =
sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE

  database_connection =
mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock
-

Then when I type sh run.sh I get this:

-
wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh
Traceback (most recent call last):
   File ./scripts/paster.py, line 34, in module
 command.run()
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
line 84, in run
 invoke(command, command_name, options, args[1:])
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
line 123, in invoke
 exit_code = runner.run(args)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
line 218, in run
 result = self.command()
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py,
line 276, in command
 relative_to=base, global_conf=vars)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py,
line 313, in loadapp
 **kw)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 204, in loadapp
 return loadobj(APP, uri, name=name, **kw)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 224, in loadobj
 global_conf=global_conf)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 248, in loadcontext
 global_conf=global_conf)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 278, in _loadconfig
 return loader.get_context(object_type, name, global_conf)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 413, in get_context
 section)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 458, in _context_from_explicit
 value = import_string(found_expr)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
line 18, in import_string
 return pkg_resources.EntryPoint.parse(x=+s).load(False)
   File
/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py,
line 1997, in parse
 src
ValueError: (EntryPoint must be in 'name=module:attrs [extras]'
format, 'x=galaxy.web.buildapp:app_factory\ndatabase_connection =
mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock')

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and other Galaxy lists, please use the interface at:

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