Re: [galaxy-dev] Galaxy instance file upload problem

[Hans-Rudolf Hotz]

Hi Bongsoo

we had once a similar situation with one of our development Galaxy 
installations. This was due to a change in the proxy settings of the server.



Regards, Hans-Rudolf

On 10/17/2014 01:06 AM, Bongsoo Park wrote:

Aysam,

Thanks for your reply. It works well on usegalaxy.org
, but it doesn't work in the Galaxy instance I've
developed. I downloaded the latest Galaxy version, and installed on the
Redhat 6.5 system. I created a galaxy user, and just ran it as usual. I
have to update any part of the configuration? I have to allow any
specific port to use file upload function? Thanks!

Best,
Bongsoo

On Thu, Oct 16, 2014 at 6:25 PM, Aysam Guerler mailto:aysam.guer...@gmail.com>> wrote:

Hey Bongsoo,

Does this happen on usegalaxy.org ? Also does
this happen with other files too?

Thanks,
Sam

On Thu, Oct 16, 2014 at 2:49 PM, Bongsoo Park mailto:bx...@psu.edu>> wrote:

Hi folks,

I encountered the problem in file upload. The error message is
like below
'Failed: Not found (404)'. Attached is the screen shot for this
error message. Any idea? Thanks!

Best,
Bongsoo



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Re: [galaxy-dev] Set a new metadata attribute

[Hans-Rudolf Hotz]

Hi Nikos

As a 'quick and dirty' work-around, I suggest generating in addition to 
the output file a 'log' file, which can be read by the subsequent tool.


Hans-Rudolf



On 09/26/2014 04:54 PM, Peter Cock wrote:

On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos
 wrote:

Hi all,

In a tool that I am writting I want to pass an input parameter value
(string) into the output file's metadata. Meaning that one of the tool
parameters is a barcode signature, 'NNWTGXN' for example. I want that
attribute to be stored somehow in the output file in order to be read by a
subsequent tool without the user having to set that parameter again.

The files I'll be working with are in FASTQ, BAM and tabular format.

Is it possible?

Bests,
Nikos


Your code can write the value directly into an output file
(e.g. one of the SAM/BAM headers might work), but I
don't think there is anything suitable within Galaxy for
re-exporting the parameter value as an input parameter
for a future tool.

However, at the workflow level you can set variables -
might that be a way forward?

https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit

Peter
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Re: [galaxy-dev] Tool Errors

[Hans-Rudolf Hotz]

On 09/12/2014 05:11 PM, Calvin Morrison wrote:

The stderr and stdout is empty, according to galaxy.

here is paster.log output for quikr when i run it.


galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if
user == "user"   quikr -v -k 0 -s
/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i
/data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o
/data/galaxy/galaxy-dist/database/files/000/dataset_104.dat   # else
quikr -v -k 0 -s
"/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i
/data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o
/data/galaxy/galaxy-dist/database/files/000/dataset_104.dat# end if

that doesn't really seem all that helpful though.



Actually, it is very helpful, isn't-t? It shows that the command tag 
from your xml file is not properly executed.




my xml file:



 

 # if $qdb.dbtype == "user"
 quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output}
 # else
 quikr -v -k 0 -s
"${qdb.dbname}${qdb.dbsize}".__mat.gz -i ${input} -o
${output}
 # end if

 




try removing the spaces between "#" and "if", "#" and "else", and "#" 
and "end if". And re-load the tool configuration.


See also: 
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cwhen.3E_tag_set



Hope this helps

Hans-Rudolf
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[galaxy-dev] Solved - Re: testing the visualization plugins

[Hans-Rudolf Hotz]

Hi all

First of all, a big Thanks to Carl who helped me fixing this problem.

So as a summary for all, the problem was caused by a datatype (an 
extension to tabular), I manually added to "datatypes_conf.xml"


Removing the datatype fixed the problem. I couldn't identify a syntax 
problem, neither in "datatypes_conf.xml" nor in 
"~/lib/galaxy/datatypes/registry.py" and 
"~/lib/galaxy/datatypes/tabular.py". However, renaming it (in all three 
files) fixed it as well.


Regards, Hans-Rudolf
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Re: [galaxy-dev] error with multi dataset tool run

[Hans-Rudolf Hotz]

Hi Robert

Are you using the built in SQLite database ?

Hans-Rudolf

On 08/31/2014 01:27 AM, Robert Baertsch wrote:

I submitted 13 fastq files to tophat2 using DRMAA and got this error.
  Is it fatal?   BTW: This is a super cool feature.

I’m running the following version of galaxy-dist.

changeset:   14212:91547729ffde
branch:  stable
tag: tip
user:Nate Coraor mailto:n...@bx.psu.edu>>
date:Fri Aug 29 14:00:23 2014 -0400
summary: Update tag latest_2014.08.11 for changeset ea12550fbc34

-Robert


There were errors setting up 2 submitted job(s):

  * *Error executing tool: (OperationalError) database is locked
u'UPDATE history_dataset_association SET update_time=?, name=?,
blurb=? WHERE history_dataset_association.id = ?' ('2014-08-30
23:14:44.683957', 'Tophat2 on data 7: insertions', 'queued', 137)*
  * *Error executing tool: (OperationalError) database is locked
u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?'
('2014-08-30 23:15:57.204718', 'queued', 446)*




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Re: [galaxy-dev] testing the visualization plugins

[Hans-Rudolf Hotz]

Hi Carl

Thanks for your help  - unfortunately no success so far



Let's try two things:

*First*, let's clear the browser cache to rule out that annoyance:


This didn't change anything. I have also tried different computers and 
different browsers




*Second*, let's see what the server ends up sending the client for
visualizations:


it just looks like this:

"visible": true,
"visualizations": [
{
"embeddable": false,
"href": 
"/visualization/trackster?dataset_id=b1c72d84f3501797&dbkey=%3F&hda_ldda=hda", 


"html": "Trackster",
"target": "_top"
}
]
}


Hans-Rudolf


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Re: [galaxy-dev] testing the visualization plugins

[Hans-Rudolf Hotz]

Hi Carl


What was the datatype (listed as 'format') of the dataset you tested
with here?:

However, if I hoover over the bar-plot icon, "Visualize in
Trackster" pops up (instead of just "Visualize")


any data type, eg wig, tabular, bed, etc

I currently have: 'result_type="datatype">data.Data'

in  ~/config/plugins/visualizations/trackster/config/trackster.xml

If I change that to 'result_type="datatype">interval.Interval'  (and do 
a restart), I lose the bar-plot icon for wig and tabular. It is still 
there for the bed file in the history.





Do the 'charts' and 'scatterplot' visualizations show up in the
visualization icon popup menu when you check on an interval or bed datatype?


They never show up, I don't get the menu when I click on the bar-plot 
icon (for bed and/or interval data typ). It goes straight to the 
Trackster page, where, I am asked to define the Browser name and the 
Reference genome.


Hans-Rudolf



Thanks for the report and any info you can provide,
Carl



On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi

As part of my upgrade/testing work, I am looking at the
visualization plugins.

In a new galaxy installation ("latest_2014.08.11"), they (ie
'Charts', 'Scatterplot', and 'Trackster')  seem to work fine.


All I have done was:

  - I defined the visualization_plugins___directory in the
universe_wsgi.ini file

If I comment-out this line, I only get trackster, when I click on
the icon which looks like a bar-plot



Next, I have tried it on our development server (after I have
upgraded from "release_2014.04.14" to "latest_2014.08.11"). I
changed the universe_wsgi.ini file.

I the logs I get:

galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,639
VisualizationsRegistry, loaded plugin: charts
galaxy.web.base.__pluginframework WARNING 2014-08-27 09:43:45,641
VisualizationsRegistry, plugin load failed or disabled:
./config/plugins/__visualizations/circster. Skipping...
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,655
VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,657
VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,675
VisualizationsRegistry, loaded plugin: scatterplot
galaxy.web.base.__pluginframework WARNING 2014-08-27 09:43:45,677
VisualizationsRegistry, plugin load failed or disabled:
./config/plugins/__visualizations/sweepster. Skipping...
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,679
VisualizationsRegistry, loaded plugin: trackster

wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me.


However, if I hoover over the bar-plot icon, "Visualize in
Trackster" pops up (instead of just "Visualize"), and when I click
on it I get straight to the Trackster page, where, I am asked to
define the Browser name and the Reference genome. No links for
'Charts' and 'Scatterplot'.

On the other hand, the plug in infrastructure seems to work: If I
change
~/config/plugins/__visualizations/trackster/__config/trackster.xml I
see the effects, ie if I change

result_type="datatype">data.__Data<
to
result_type="datatype">__interval.Interval

I can restrict the visualization to only the interval data.


Somehow, I am running a mixture of the 'old' and the 'new'
visualization set-up ?

Has anyone seen similar problems when testing the new plug in
infrastructure on an old/upgraded Galaxy installation

Thank you very much for any hints and help


Hans-Rudolf







--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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[galaxy-dev] testing the visualization plugins

[Hans-Rudolf Hotz]

Hi

As part of my upgrade/testing work, I am looking at the visualization 
plugins.


In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts', 
'Scatterplot', and 'Trackster')  seem to work fine.



All I have done was:

 - I defined the visualization_plugins_directory in the
   universe_wsgi.ini file

If I comment-out this line, I only get trackster, when I click on the 
icon which looks like a bar-plot




Next, I have tried it on our development server (after I have upgraded 
from "release_2014.04.14" to "latest_2014.08.11"). I changed the 
universe_wsgi.ini file.


I the logs I get:

galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639 
VisualizationsRegistry, loaded plugin: charts
galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641 
VisualizationsRegistry, plugin load failed or disabled: 
./config/plugins/visualizations/circster. Skipping...
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655 
VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657 
VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675 
VisualizationsRegistry, loaded plugin: scatterplot
galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677 
VisualizationsRegistry, plugin load failed or disabled: 
./config/plugins/visualizations/sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679 
VisualizationsRegistry, loaded plugin: trackster


wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me.


However, if I hoover over the bar-plot icon, "Visualize in Trackster" 
pops up (instead of just "Visualize"), and when I click on it I get 
straight to the Trackster page, where, I am asked to define the Browser 
name and the Reference genome. No links for 'Charts' and 'Scatterplot'.


On the other hand, the plug in infrastructure seems to work: If I change 
~/config/plugins/visualizations/trackster/config/trackster.xml I see the 
effects, ie if I change


result_type="datatype">data.Data<
to
result_type="datatype">interval.Interval

I can restrict the visualization to only the interval data.


Somehow, I am running a mixture of the 'old' and the 'new' visualization 
set-up ?


Has anyone seen similar problems when testing the new plug in 
infrastructure on an old/upgraded Galaxy installation


Thank you very much for any hints and help


Hans-Rudolf







--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] problems with database migration 119 -> 120

[Hans-Rudolf Hotz]

Hi John

Thanks for the insights


Hi Iyad

Yes, the user account has the ability to drop and alter tables.


Hans-Rudolf


On 08/26/2014 03:08 PM, John Chilton wrote:

Well it looks like the migration file has these columns listed in a
different order than the mapping Galaxy uses - and the order yours
appeared in were the ones from Galaxy's mapping file. So somehow
Galaxy is automatically creating those tables prior to running the
migration based on the code in Galaxy proper. That is odd.

Ultimately though - I don't think it is harmful that the order is
wrong since Galaxy always references the columns by name instead of
order. I would be more concerned that you aren't getting the right
indices / foreign keys - but it looks like you are still on MyISAM so
you aren't going to get a ton of forced integrity anyway (and maybe
this is why these errors have been okay in the past?).

-John

On Tue, Aug 26, 2014 at 8:52 AM, Kandalaft, Iyad
 wrote:

I've ran into other mysql problems but never anything like that.

This is just a hunch and not based on anything concrete, but using an outdated version of 
sqlalchemy is probably not helping things.  We're talking 2 migrations.  Are they even 
implementing fixes for 0.7 anymore?  It is odd you would ever get "Table already 
exists" since the ORM's job is to ensure the model consistency in the database.  Why 
it would try to create the table before it checks for its existence is beyond me.

You might want to make sure that the database user account has the ability to 
drop and alter tables.  It may be that it tried to revert a failed upgrade and 
it wasn't able to.

Iyad Kandalaft



-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hans-Rudolf Hotz
Sent: Tuesday, August 26, 2014 5:22 AM
To: 
Subject: [galaxy-dev] problems with database migration 119 -> 120

Hi all

I am in the process of updating our galaxy servers (from "release_2014.04.14" to 
"latest_2014.08.11").


when I execute

~/lib/galaxy/model/migrate/versions/0120_dataset_collections.py

as part of the 'manage_db.sh upgrade' I run into a bizarre error:

First, it produces 10 "Mysql 1050 Error 'Table already exists' ", I have
encountered this before, and usually everything is fine. The table gets
created and for whatever reason, the command get's executed a second
time - no big deal.

However, this time for two of those ten table the situation has been
different. As usual, I have checked all the tables (where I got the
errors) with the MySQL command describe .

For two tables:

history_dataset_collection_association

library_dataset_collection_association

the order of the columns was wrong (ie did not correspond to the order
in the create statement) - see below for example.

I have dropped the tables and executed the create statements manually,
everything seems fine, eg



mysql> describe library_dataset_collection_association;
+---+--+--+-+-++
| Field | Type | Null | Key | Default | Extra  |
+---+--+--+-+-++
| id| int(11)  | NO   | PRI | NULL| auto_increment |
| collection_id | int(11)  | YES  | MUL | NULL||
| folder_id | int(11)  | YES  | MUL | NULL||
| name  | varchar(255) | YES  | | NULL||
| deleted   | tinyint(1)   | YES  | | NULL||
+---+--+--+-+-++
5 rows in set (0.00 sec)

mysql> drop table library_dataset_collection_association;
Query OK, 0 rows affected (0.02 sec)

mysql> CREATE TABLE library_dataset_collection_association (
  -> id INTEGER NOT NULL AUTO_INCREMENT,
  -> collection_id INTEGER,
  -> name VARCHAR(255),
  -> deleted BOOL,
  -> folder_id INTEGER,
  -> PRIMARY KEY (id),
  -> FOREIGN KEY(collection_id) REFERENCES dataset_collection (id),
  -> CHECK (deleted IN (0, 1)),
  -> FOREIGN KEY(folder_id) REFERENCES library_folder (id)
  -> );
Query OK, 0 rows affected (0.01 sec)

mysql> describe library_dataset_collection_association;
+---+--+--+-+-++
| Field | Type | Null | Key | Default | Extra  |
+---+--+--+-+-++
| id| int(11)  | NO   | PRI | NULL| auto_increment |
| collection_id | int(11)  | YES  | MUL | NULL||
| name  | varchar(255) | YES  | | NULL||
| deleted   | tinyint(1)   | YES  | | NULL||
| folder_id | int(11)  | YE

[galaxy-dev] problems with database migration 119 -> 120

[Hans-Rudolf Hotz]

Hi all

I am in the process of updating our galaxy servers (from 
"release_2014.04.14" to "latest_2014.08.11").



when I execute

~/lib/galaxy/model/migrate/versions/0120_dataset_collections.py

as part of the 'manage_db.sh upgrade' I run into a bizarre error:

First, it produces 10 "Mysql 1050 Error 'Table already exists' ", I have 
encountered this before, and usually everything is fine. The table gets 
created and for whatever reason, the command get's executed a second 
time - no big deal.


However, this time for two of those ten table the situation has been 
different. As usual, I have checked all the tables (where I got the 
errors) with the MySQL command describe .


For two tables:

history_dataset_collection_association

library_dataset_collection_association

the order of the columns was wrong (ie did not correspond to the order 
in the create statement) - see below for example.


I have dropped the tables and executed the create statements manually, 
everything seems fine, eg




mysql> describe library_dataset_collection_association;
+---+--+--+-+-++
| Field | Type | Null | Key | Default | Extra  |
+---+--+--+-+-++
| id| int(11)  | NO   | PRI | NULL| auto_increment |
| collection_id | int(11)  | YES  | MUL | NULL||
| folder_id | int(11)  | YES  | MUL | NULL||
| name  | varchar(255) | YES  | | NULL||
| deleted   | tinyint(1)   | YES  | | NULL||
+---+--+--+-+-++
5 rows in set (0.00 sec)

mysql> drop table library_dataset_collection_association;
Query OK, 0 rows affected (0.02 sec)

mysql> CREATE TABLE library_dataset_collection_association (
-> id INTEGER NOT NULL AUTO_INCREMENT,
-> collection_id INTEGER,
-> name VARCHAR(255),
-> deleted BOOL,
-> folder_id INTEGER,
-> PRIMARY KEY (id),
-> FOREIGN KEY(collection_id) REFERENCES dataset_collection (id),
-> CHECK (deleted IN (0, 1)),
-> FOREIGN KEY(folder_id) REFERENCES library_folder (id)
-> );
Query OK, 0 rows affected (0.01 sec)

mysql> describe library_dataset_collection_association;
+---+--+--+-+-++
| Field | Type | Null | Key | Default | Extra  |
+---+--+--+-+-++
| id| int(11)  | NO   | PRI | NULL| auto_increment |
| collection_id | int(11)  | YES  | MUL | NULL||
| name  | varchar(255) | YES  | | NULL||
| deleted   | tinyint(1)   | YES  | | NULL||
| folder_id | int(11)  | YES  | MUL | NULL||
+---+--+--+-+-++
5 rows in set (0.00 sec)

mysql>



Has anyone else (among those few who are still using MySQL) seen 
something similar?



Regards, Hans-Rudolf


PS: Please don't make any comments about the fact, that I should change
to PostgreSQL. I am more than aware of that, and eventually, I will
do it.   ;)




--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Settings multiple Genome Indices

[Hans-Rudolf Hotz]

On 07/28/2014 10:02 AM, Geert Vandeweyer wrote:

If I understand you correctly, would this mean generating a custom .loc
file for this tool containing the concatenated paths? Or can I
concatenate paths from different .loc files somehow, which would allow
me to use the default loc files?




This would require a custom .loc  file

Hans-Rudolf


Geert

On 07/28/2014 09:33 AM, Hans-Rudolf Hotz wrote:

Hi Geert

A simple solution might be: you hand over a string containing all
three paths to your wrapper, and then the wrapper splits the string
into the three individual paths.


Hans-Rudolf






On 07/27/2014 04:44 PM, Geert Vandeweyer wrote:

Hi,

I'm working on tool wrapper that needs three reference genome locations
(2bit/lastz, all_fasta and novoalign). Is there a way to fetch the three
paths from the loc files using a single select box? I've looked around
in a couple of tool wrappers on the toolshed, but could find any leads.
Something like the following would be ok:

Select options from all_fasta.loc
 -> upon change, set hidden variables to novoalign.loc +
lastz_seqs.loc using a filter tag or something against the selected
options from all_fasta.

Even more simple : access in the command tag like:
--novoidx novoalign-loc.options[dbkey=$input.dbkey,path] --fasta
all_fasta-loc[dbkey=$input.dbkey,path] etc , using the dbkey from the
input file (which is a bam file in this case)

In this case, error handling should come from the tool, if one of the
indices is missing.

I'm currently using three selection boxes, but that looks a but
redundant to the user, as they all have to select the same thing.

Best,

Geert





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Re: [galaxy-dev] Settings multiple Genome Indices

[Hans-Rudolf Hotz]

Hi Geert

A simple solution might be: you hand over a string containing all three 
paths to your wrapper, and then the wrapper splits the string into the 
three individual paths.



Hans-Rudolf






On 07/27/2014 04:44 PM, Geert Vandeweyer wrote:

Hi,

I'm working on tool wrapper that needs three reference genome locations
(2bit/lastz, all_fasta and novoalign). Is there a way to fetch the three
paths from the loc files using a single select box? I've looked around
in a couple of tool wrappers on the toolshed, but could find any leads.
Something like the following would be ok:

Select options from all_fasta.loc
 -> upon change, set hidden variables to novoalign.loc +
lastz_seqs.loc using a filter tag or something against the selected
options from all_fasta.

Even more simple : access in the command tag like:
--novoidx novoalign-loc.options[dbkey=$input.dbkey,path] --fasta
all_fasta-loc[dbkey=$input.dbkey,path] etc , using the dbkey from the
input file (which is a bam file in this case)

In this case, error handling should come from the tool, if one of the
indices is missing.

I'm currently using three selection boxes, but that looks a but
redundant to the user, as they all have to select the same thing.

Best,

Geert


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Re: [galaxy-dev] Local deployments of galaxy

[Hans-Rudolf Hotz]

Hi David

There is another number, which might help you:

- there are over 1000 people on the dev-mailing list
  (https://wiki.galaxyproject.org/GalaxyProject/Statistics#Membership)


assuming there are two galaxy admins per site - wishful thinking ;) - 
and each site has on average two Galaxy servers running...you end up 
with ~1000 Galaxy servers in the Universe.



Hans-Rudolf


On 07/24/2014 07:02 PM, Martin Čech wrote:

There is a list of the ones that reached back to us and are publicly
accessible (~60): https://wiki.galaxyproject.org/PublicGalaxyServers

As of private ones there is no good clue as Galaxy does not call home.

M.


On Thu, Jul 24, 2014 at 12:55 PM, Lapointe, David
mailto:david.lapoi...@tufts.edu>> wrote:

Not exactly a dev question, but I was asked recently how many sites
are running galaxy. The wiki  page listing deployments seems not to
reflect the actual number, since may are most likely private.

Is there an estimate?
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospatial Technology Services
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667
http://it.tufts.edu

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Re: [galaxy-dev] Jobs stay queued

[Hans-Rudolf Hotz]

On 07/23/2014 02:13 PM, julie dubois wrote:

I'm using a MySQL database !!!
But may be such database-lock can appear because of my universe.ini
configuration file.
Here it's the lines concerning the database :

database_engine_option_pool_size = 10
database_engine_option_max_overflow = 20
database_engine_option_pool_recycle = -1
database_engine_option_strategy = threadlocal


Can one of these parameters be at the origin of my problem ?




we are also using MySQL, but we use the suggested setting:

database_engine_option_pool_recycle = 7200


though, i don't think this is related to your problem. Or did you get 
the error: "MySQL server has gone away" in the galaxy log file?





If yes, when I'll restart Galaxy, the queued jobs will be in a staying
state with the capacity to become in a running state ?
Or they will be in error state and I should restart the process as new jobs ?


I don't know, I don't have enough experience with queued workflow jobs 
and what is happening with them during a re-start. I am sorry, I can't 
be of much further help.  Maybe someone else on the list?


Hans-Rudolf






Thanks.

Julie

2014-07-23 12:55 GMT+02:00 Hans-Rudolf Hotz :



On 07/23/2014 12:05 PM, julie dubois wrote:


Hi Hans-Rudolf,
Thanks for your answer.
I've launched lot of jobs since monday. And some jobs were finished
and some jobs never started.
In "Manage jobs" I can see jobs queued because they need inputs which
are queued, so I think it's normal.

But other jobs are described like this :

9554   user_login   0 hours agosamtools_flagstatnew23199
ok, 23243 okNoneNoneNone
The two necessary inputs for this job (23199 and 2343) are ok and the
job doesn't run.


Another mysterious line is :

9561  user_login0 hours ago fastqc   new  Unable to
determine inputs  None NoneNone

After check this job in my history, I'm sure that the input of this
job is green and really available. Why can galaxy not determine inputs
?
Finally, in "Manage Jobs" there are only jobs queued. No jobs running.

Any idea ?



I have one suspicion:

which database are you using?
If you are just using the built in SQlite you might have run in a
database-lock?  Because you have submitted too many jobs at once?

In this case, I guess, the only way to recover is to re-start...

Hans-Rudolf




Thanks
Julie

2014-07-23 11:35 GMT+02:00 Hans-Rudolf Hotz :


Hi Julie

Are there any jobs running at all?  What do you get when you click on
"Manage jobs" in the admin menu?  Maybe you have some old jobs 'running'
which are now blocking your queue?

Hans-Rudolf



On 07/23/2014 11:14 AM, julie dubois wrote:



Hi all,
I've seen several posts for jobs which stay queued and never start
with an installation of galaxy on a cluster.
But our installation is just a local instance of galaxy in 1 PC and I
have more than 100 jobs which stay queued and never start.

How can I debug this problem (my version of galaxy is the latest
2june2014).

And is it possible to run those jobs without restart galaxy because it
would be very long to rerun each job manually after reloading galaxy.

Thanks.

Julie
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Re: [galaxy-dev] Jobs stay queued

[Hans-Rudolf Hotz]

On 07/23/2014 12:05 PM, julie dubois wrote:

Hi Hans-Rudolf,
Thanks for your answer.
I've launched lot of jobs since monday. And some jobs were finished
and some jobs never started.
In "Manage jobs" I can see jobs queued because they need inputs which
are queued, so I think it's normal.

But other jobs are described like this :

9554   user_login   0 hours agosamtools_flagstatnew23199
ok, 23243 okNoneNoneNone
The two necessary inputs for this job (23199 and 2343) are ok and the
job doesn't run.


Another mysterious line is :

9561  user_login0 hours ago fastqc   new  Unable to
determine inputs  None NoneNone

After check this job in my history, I'm sure that the input of this
job is green and really available. Why can galaxy not determine inputs
?
Finally, in "Manage Jobs" there are only jobs queued. No jobs running.

Any idea ?


I have one suspicion:

which database are you using?
If you are just using the built in SQlite you might have run in a 
database-lock?  Because you have submitted too many jobs at once?


In this case, I guess, the only way to recover is to re-start...

Hans-Rudolf



Thanks
Julie

2014-07-23 11:35 GMT+02:00 Hans-Rudolf Hotz :

Hi Julie

Are there any jobs running at all?  What do you get when you click on
"Manage jobs" in the admin menu?  Maybe you have some old jobs 'running'
which are now blocking your queue?

Hans-Rudolf



On 07/23/2014 11:14 AM, julie dubois wrote:


Hi all,
I've seen several posts for jobs which stay queued and never start
with an installation of galaxy on a cluster.
But our installation is just a local instance of galaxy in 1 PC and I
have more than 100 jobs which stay queued and never start.

How can I debug this problem (my version of galaxy is the latest
2june2014).

And is it possible to run those jobs without restart galaxy because it
would be very long to rerun each job manually after reloading galaxy.

Thanks.

Julie
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Re: [galaxy-dev] Jobs stay queued

[Hans-Rudolf Hotz]

Hi Julie

Are there any jobs running at all?  What do you get when you click on 
"Manage jobs" in the admin menu?  Maybe you have some old jobs 'running' 
which are now blocking your queue?


Hans-Rudolf


On 07/23/2014 11:14 AM, julie dubois wrote:

Hi all,
I've seen several posts for jobs which stay queued and never start
with an installation of galaxy on a cluster.
But our installation is just a local instance of galaxy in 1 PC and I
have more than 100 jobs which stay queued and never start.

How can I debug this problem (my version of galaxy is the latest 2june2014).

And is it possible to run those jobs without restart galaxy because it
would be very long to rerun each job manually after reloading galaxy.

Thanks.

Julie
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Re: [galaxy-dev] cleanup_datasets.py not deleting files...

[Hans-Rudolf Hotz]

On 07/17/2014 12:38 PM, neil.burd...@csiro.au wrote:

Thanks. Is there a script that will delete all files older than a certain date 
even if not marked as deleted by the user?



I am not aware of such a script

Hans-Rudolf


Thanks
Neil

From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Thursday, July 17, 2014 5:42 PM
To: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...

Hi Neil

The cleanup_datasets.py script only removes the files if older than the
time given (you did this, ie older than 20 days) AND if the dataset has
been marked as 'deleted' by the user - have you done that?

see also:
https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets


Hope this helps
Hans-Rudolf


On 07/17/2014 02:42 AM, neil.burd...@csiro.au wrote:

Hi,
  I'm trying to use the cleanup_datasets.py file to remove all files
on my system older than 20 days. My crontab looks like this:

# m h  dom mon dow   command
34 10 * * * cd /export/barium-data3/galaxy-suvr && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -1
  > /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -2
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -3
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -5
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -4
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -6
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1

The crontab executes and the contents of
/home/galaxy/crontab_purge_milxcloud.log is:

cat /home/galaxy/crontab_purge_milxcloud.log
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:02 - Handling stuff older than 20 days
Datasets will NOT be removed from disk.

Deleted 0 histories
Elapsed time:  0.170083045959
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:02 - Handling stuff older than 20 days
Datasets will be removed from disk.

Purged 0 histories.
Elapsed time:  0.174137830734
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:03 - Handling stuff older than 20 days
Datasets will be removed from disk.

Purged 0 datasets
Freed disk space:  0
Elapsed time:  0.168104887009
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:04 - Handling stuff older than 20 days
Datasets will be removed from disk.

# Purged 0 folders.
Elapsed time:  0.168635129929
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:05 - Handling stuff older than 20 days
Datasets will be removed from disk.

# Purged 0 libraries .
Elapsed time:  0.166506052017
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:06 - Handling stuff older than 20 days
Datasets will be removed from disk.

Examined 0 datasets, marked 0 datasets and 0 dataset instances (HDA) as
deleted
Total elapsed time:  0.00744795799255
##

However, today is the 17th July and when I look into  the database
directory i.e. ~/database/files/000 I still have files from the 18th
June so older than 20 days i.e.:

drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_213_files
-rw-r--r-- 1 galaxy nogroup 1061 Jun 18 09:19 dataset_213.dat
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_215_files
-rw-r--r-- 1 galaxy nogroup  270 Jun 18 09:19 dataset_215.dat
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_221_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_219_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_220_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_222_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_218_files
-rw-r--r-- 1 galaxy nogroup  994 Jun 18 09:19 dataset_216.dat
-rw-r--r-- 1 galaxy nogroup  161 Jun 18 09:19 dataset_214.dat

Am I doing something wrong? Using wrong arguments/file etc ?

Thanks
Neil


__

Re: [galaxy-dev] cleanup_datasets.py not deleting files...

[Hans-Rudolf Hotz]

Hi Neil

The cleanup_datasets.py script only removes the files if older than the 
time given (you did this, ie older than 20 days) AND if the dataset has 
been marked as 'deleted' by the user - have you done that?


see also:
https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets


Hope this helps
Hans-Rudolf


On 07/17/2014 02:42 AM, neil.burd...@csiro.au wrote:

Hi,
 I'm trying to use the cleanup_datasets.py file to remove all files
on my system older than 20 days. My crontab looks like this:

# m h  dom mon dow   command
34 10 * * * cd /export/barium-data3/galaxy-suvr && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -1
 > /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -2
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -3
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -5
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -4
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -6
-r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1

The crontab executes and the contents of
/home/galaxy/crontab_purge_milxcloud.log is:

cat /home/galaxy/crontab_purge_milxcloud.log
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:02 - Handling stuff older than 20 days
Datasets will NOT be removed from disk.

Deleted 0 histories
Elapsed time:  0.170083045959
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:02 - Handling stuff older than 20 days
Datasets will be removed from disk.

Purged 0 histories.
Elapsed time:  0.174137830734
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:03 - Handling stuff older than 20 days
Datasets will be removed from disk.

Purged 0 datasets
Freed disk space:  0
Elapsed time:  0.168104887009
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:04 - Handling stuff older than 20 days
Datasets will be removed from disk.

# Purged 0 folders.
Elapsed time:  0.168635129929
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:05 - Handling stuff older than 20 days
Datasets will be removed from disk.

# Purged 0 libraries .
Elapsed time:  0.166506052017
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:06 - Handling stuff older than 20 days
Datasets will be removed from disk.

Examined 0 datasets, marked 0 datasets and 0 dataset instances (HDA) as
deleted
Total elapsed time:  0.00744795799255
##

However, today is the 17th July and when I look into  the database
directory i.e. ~/database/files/000 I still have files from the 18th
June so older than 20 days i.e.:

drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_213_files
-rw-r--r-- 1 galaxy nogroup 1061 Jun 18 09:19 dataset_213.dat
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_215_files
-rw-r--r-- 1 galaxy nogroup  270 Jun 18 09:19 dataset_215.dat
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_221_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_219_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_220_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_222_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_218_files
-rw-r--r-- 1 galaxy nogroup  994 Jun 18 09:19 dataset_216.dat
-rw-r--r-- 1 galaxy nogroup  161 Jun 18 09:19 dataset_214.dat

Am I doing something wrong? Using wrong arguments/file etc ?

Thanks
Neil


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Re: [galaxy-dev] Unable to update to latest version of galaxy

[Hans-Rudolf Hotz]

Hi Eleanor


I was running into the same problem when I did the updates for our 
servers (from release_2013.11.04 to release_2014.04.14), eg:


...
pkg_resources.VersionConflict: (pycrypto 2.0.1 
(/usr/lib64/python2.6/site-packages), 
Requirement.parse('pycrypto>=2.1,!=2.4'))

Fetch failed.


I solved it by deleting the contents of ~/galaxy_dist/eggs/ and fetched 
all eggs again (not just the new/updated ones). This somehow solved the 
problem, by using the (re-fetched) 'pycrypto' from ~/galaxy_dist/eggs/ 
instead of the one provided by the system.




Regards, Hans-Rudolf







On 07/17/2014 04:35 AM, Eleanor Morgan wrote:

Hi all,

I am new to galaxy.  We have a local install that we intend to turn into
a production server at some stage.  We initially installed galaxy using
the April 2014 version.  We set up a Virtual Python Environment
following the instructions set out on this page:

https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment

When I updated to the June version of galaxy and tried to start up the
server using the recommended shell script placed in /etc/init.d I got
the following error message:

Starting galaxy...

Some eggs are out of date, attempting to fetch...

Traceback (most recent call last):

   File "./scripts/fetch_eggs.py", line 37, in 

 c.resolve() # Only fetch eggs required by the config

   File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in
resolve

 egg.resolve()

   File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in
resolve

 return self.version_conflict( e.args[0], e.args[1] )

   File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in
version_conflict

 r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
env, egg.fetch )

   File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 550,
in resolve

 raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pycrypto 2.0.1
(/usr/lib64/python2.6/site-packages),
Requirement.parse('pycrypto>=2.1,!=2.4'))

Fetch failed.

…done.


This error message implies that I need to update pycrypto on our system,
but my understanding is that the virtual python environment takes care
of these sorts of dependencies. Can someone please advise?  Here are two
series of commands that I tried to start the system:


First attempt:

sudo bash

/etc/init.d/galaxy stop

su - galaxy

cd /galaxy/galaxy-dist

hg pull

hg update latest_2014.06.02

exit

/etc/init.d/galaxy start


After galaxy start failed I tried:

su – galaxy

cd /galaxy

. ./galaxy_env/bin/activate

cd galaxy_dist

sh run.sh


I also tried reinstalling the virtual environment to no avail.


Regards,

Eleanor





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[galaxy-dev] Swiss-German Galaxy Tour: Sep 30th to Oct 2nd - Training day - Workshop - Developers day

[Hans-Rudolf Hotz]

Dear all


After the big success of the "Swiss Galaxy Workshop" two years ago, we 
are going to organize a similar event again in Bern on Wednesday October 
first.


https://wiki.galaxyproject.org/Events/Switzerland2014

Like last time, the aim is to discuss the status of the Galaxy project,
new developments, interface to other systems, extensions and best
practice in reproducible research. We also welcome participants who are
using workflow management systems other than Galaxy and tool developers
who are looking for such systems to offer their tools to a wider audience.

This year, the workshop will be part of a three day event
(https://wiki.galaxyproject.org/Events/SG2014):

 - Prior to the workshop, we run a Galaxy training/demo Day
 on Tuesday September, 30th also in Bern (Switzerland)

 - Following the workshop, we organize a Developers Day
 on Thursday, October 2nd in Freiburg (Germany)


The Developers Day is aimed at Galaxy hackers, tool and visualization 
developers. The format is still in discussion, but we intend to talk about:

 - defining tools and data sources to Galaxy
 - using Galaxy with different data stores (ObjectStore)
 - the Galaxy API

Similar to the Workshop the day before, presentations by attendees of 
the Developers Day are highly encouraged. Titles can be submitted at 
registration time.



Registration is free, but space is limited. We recommend you register 
soon to secure your spot on one, two or all three days of the SG2014Tour:


http://www.surveymonkey.com/s/SG2014Tour


Looking forward to see many of you in Bern and Freiburg

Regards, Bjoern and Hans-Rudolf



--

Hans-Rudolf Hotz, PhD
Bioinformatics Support

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


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Re: [galaxy-dev] Galaxy mobile site

[Hans-Rudolf Hotz]

Hi Mark

There used to be a nice one: try adding '/mobile" to your galaxy url.

It is still kind of working (just without the graphics), and it is 
sufficient to monitor jobs.


Hans-Rudolf



There used to be one.

On 06/26/2014 08:03 AM, MF Rogers wrote:

I hope this isn't a FAQ; I have not yet found the question (or answer)
online, though I can't imagine I'm the first to ask:

Are there plans to make a mobile version of the Galaxy website?  Many of
the biologists with whom I work would like to be able to monitor and
start Galaxy jobs from their iPhones (or other smart phone).  While it
is possible to do so using the regular website, a mobile-specific site
could make it easier.

We searched in vain for an app, but I gather that would be a headache to
maintain with such a dynamic website.  A mobile site seems the right
approach, unless there are good reasons not to try it?

We may experiment with creating one for our own local Galaxy
installation, but would prefer to use existing code if it's available.

Many thanks,
--
Dr. Mark Rogers
Intelligent Systems Laboratory
Department of Engineering Mathematics
University of Bristol


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Re: [galaxy-dev] Galaxy updated botched?

[Hans-Rudolf Hotz]

On 06/12/2014 12:06 AM, John Chilton wrote:



If anyone out there has tired using Galaxy with strictly MyISAM tables
and found it untenable - by all means please chime in.



Well, due to several reasons we are (still) using  MySQL (version: 
5.1.69) with only MyISAM tables. We have been running into troubles but 
they were never related to running MyISAM.


However, I haven't done the latest Galaxy code upgrade, hence we are 
still on database version '118'. So, I am curious to see what will 
happen when I do the next upgrade (after GCC).


Also, on my list of things to do for this year is actually changing all 
our Galaxy servers from MySQL to PostgreSQL. With my current workload, I 
doubt I will manage to do this and have to postpone this 'adventure' to 
next year.



Regards, Hans-Rudolf
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Re: [galaxy-dev] ClustalW jobs aren't working

[Hans-Rudolf Hotz]

On 06/09/2014 07:33 PM, Malcolm Tobias wrote:

All,

I apologize for an off-topic question, by my update failed:

[galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg pull -u |
tee hg.pull.out

...

added 3716 changesets with 9929 changes to 2124 files (+46 heads)

...

merging lib/galaxy/app.py

merging lib/galaxy/app.py failed!

warning: conflicts during merge.

merging lib/galaxy/model/__init__.py

merging lib/galaxy/model/__init__.py failed!

warning: conflicts during merge.

merging lib/galaxy/model/mapping.py

merging lib/galaxy/model/mapping.py failed!

merging tool-data/shared/ucsc/ucsc_build_sites.txt and
tool-data/shared/ucsc/ucsc_build_sites.txt.sample to
tool-data/shared/ucsc/ucsc_build_sites.txt.sample

1528 files updated, 1 files merged, 1289 files removed, 3 files unresolved

use 'hg resolve' to retry unresolved file merges

resolve apparently can't fix this issue:

[galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg resolve --all

merging lib/galaxy/app.py

warning: conflicts during merge.

merging lib/galaxy/app.py failed!

merging lib/galaxy/model/__init__.py

warning: conflicts during merge.

merging lib/galaxy/model/__init__.py failed!

merging lib/galaxy/model/mapping.py

warning: conflicts during merge.

merging lib/galaxy/model/mapping.py failed!

What's the recommended way to fix this?



Depending on your local customization, it is not unusual to get 
unresolved files.

Open the files in an editor and complete the merge manually.


Regards, Hans-Rudolf






Thanks!

Malcolm

On Monday 09 June 2014 10:47:04 Malcolm Tobias wrote:

 >

 > Ross,

 >

 > Thanks for the response. My instance of Galaxy is indeed ancient:

 >

 > [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg tip

 > changeset: 10003:b4a373d86c51

 > tag: tip

 > parent: 10001:471484ff8be6

 > user: greg

 > date: Wed Jun 12 11:48:09 2013 -0400

 > summary: Add targets to Repository Actions menu items.

 >

 > Previous attempts at updating have been pretty painful. I'll give it
a shot and let you know whether or not this fixes the problem.

 >

 > Cheers,

 > Malcolm

 >

 > On Friday 06 June 2014 18:30:01 Ross wrote:

 > > Hi Malcolm,

 > > That error makes me think you might be running an outdated version
of galaxy code - the toolshed code has undergone extensive revision over
the last few months?

 > > I just tested that repository on a freshly updated galaxy-central
clone and it installed without drama, so I wonder what:

 > >

 > > hg tip

 > >

 > > shows?

 > >

 > > I just tested using :

 > > (vgalaxy)rlazarus@rlazarus-UX31A:~/galaxy$ hg tip

 > > changeset:   13756:84a00e4f7d06

 > > tag: tip

 > > user:Dannon Baker 

 > > date:Fri Jun 06 17:12:30 2014 -0400

 > > summary: Clarify language in DeleteIntermediateDataset PJA.

 > >

 > > If your clone is not up to date, I'd recommend completely removing
the failed installation (through the admin menu - check the box for
complete removal), shut down galaxy, backup your database, do the usual
hg pull -u dance and any necessary database upgrade steps then try a
clean install?

 > >

 > > Thanks for reporting this - if it persists on recent Galaxy code
we'll need to do some deeper investigation.

 > >

 > >

 > > On Fri, Jun 6, 2014 at 11:32 PM, Malcolm Tobias 
wrote:

 > >

 > > Ross,

 > >

 > > Thanks for the reply! Unfortunately I am the local Galaxy admin ;-)

 > >

 > > I had tried installing the clustalw tool from the toolshed, but
that failed with an error (more on that later). I disabled the local tool:

 > >

 > > [galaxy@login002 galaxy-dist]$ diff tool_conf.xml tool_conf.xml.bkup

 > > 226a227,229

 > > > 

 > > > 

 > > > 

 > >

 > > bounced galaxy in case that's necessary, then retried installing
from the toolshed. Shortly after clicking install, I get this message:

 > >

 > > Internal Server Error

 > > Galaxy was unable to sucessfully complete your request

 > >

 > > An error occurred.

 > > This may be an intermittent problem due to load or other
unpredictable factors, reloading the page may address the problem.

 > >

 > > The error has been logged to our team.

 > >

 > > The logs appear to be complaining about
'prior_installation_required' which I'm assuming means the
package_clustalw_2_1 dependency. I was able to install that, and I can
verify by looking at the local toolshed:

 > >

 > > [galaxy@login002 ~]$ ls
galaxy-toolshed/toolshed.g2.bx.psu.edu/repos/devteam/

 > > bowtie_wrappers package_clustalw_2_1 package_vcftools_0_1_11

 > > bwa_wrappers package_fastx_toolkit_0_0_13

 > >

 > > Again, I'll post the logs from when the install fails in case that
helps. Any suggestions are much appreciated.

 > >

 > > Cheers,

 > > Malcolm

 > >

 > >

 > > 10.28.56.101 - - [06/Jun/2014:08:20:38 -0500] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92
HTTP/1.1" 500 -
"http://toolshed.g2.bx

Re: [galaxy-dev] to put or not to put a tool suite into the toolshed

[Hans-Rudolf Hotz]

Hi Wolfgang


short answer:

Please, put your package into the Galaxy Tool Shed. This makes it 
visible to the whole Galaxy community and everybody can profit from it.



long answer:

I have been in the same boat. We never put the Galaxy wrappers and the 
perl scripts of our old NGS pipeline into the Tool Shed. I do feel bad 
about this. My excuse has always been that too much local customization 
would be necessary, eg making possible to store data outside the Galaxy 
directory tree. Hence, we only distributed the package as bunch of files 
on request. Obviously, there were hardly any requests.


Now we are in a similar situation. We are in the process of making our 
new R/Bioconductor based NGS pipeline available on our internal Galaxy 
server. And the code is far from being ready to be put into the Tool 
Shed. But this time we will make the effort. So the Galaxy community can 
benefit from it (@Dave Clements: Unfortunately, it won't be ready for 
Baltimore).




Regards, Hans-Rudolf




On 06/05/2014 11:52 PM, Wolfgang Maier wrote:

Dear all,
I am maintaining a (still young) suite of command line tools (written in
Python) for identification of mutations in model organism genomes
through whole-genome sequencing (https://sourceforge.net/projects/mimodd/).
MiModD aims at geneticists that do not have much background in
bioinformatics, and it's supposed to make WGS analysis for small model
organism genomes (anything from yeast to fish) possible on regular PCs,
so it's not a cloud/cluster solution.

We do support Galaxy though through a complete set of tool wrappers for
three reasons:
- to provide a graphical user interface
- to offer labs the possibility to install the software on one dedicated
machine, but run analyses from any machine (typically with Windows
installed)
- to keep analysis workflows documented and reproducible.

Currently, we advise users to take advantage of these features and
install a local instance of Galaxy even though it will be running then
only on a single desktop PC (or even just a notebook). After
installation of Galaxy our software simply copies its wrapper xmls over
to the tools folder and modifies the tool_conf file to integrate itself.
In addition, users have to install a bit of other third-party software
(samtools, snap aligner, optionally snpeff) that our code relies on.

[End of lengthy introduction]

So my question is: in what way could the package profit from being
uploaded to a Galaxy toolshed ? I guess it would mean quite some extra
work from my side since I'm not familiar with the whole procedure, so
are there benefits (visibility, ease of installation, etc.) that are
worth the effort ?

Thanks a real lot for any feedback,
Wolfgang

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Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location

[Hans-Rudolf Hotz]

As far as I know, there is no reference to the path of the datafiles in 
the 'database' (no matter whether it is SQLite, MySQL, or PostgreSQL)

- may be the Galaxy developers can confirm this?

If you wanna be on the safe side, work with a sym link, and don't change 
the entry in the  'universe_wsgi.ini' file.


Hans-Rudolf

On 06/04/2014 09:14 AM, neil.burd...@csiro.au wrote:

Thanks Hans-Rudolf,
would this also be the same case for PostgreSQL 
database? i.e. we can move the database/files somewhere else , change 
universe_wsg.ini and all would be good? There is no link from the database to 
where the flat files are stored?

cheers
Neil
________
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, June 04, 2014 5:11 PM
To: Burdett, Neil (CCI, Herston - RBWH)
Subject: Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location

Hi Neil

First a little comment: I strongly suggest to switch over to PostgreSQL.

Keep in mind that the 'database' (in your case the SQLite database) does
not contain any data. The 'database' contains just the meta data and the
users data which is required to run Galaxy.

"#file_path = database/files" is the location where the data sets are
stored. You can copy the contents of "~/database/files/ to a new
location and make the appropriate changes in 'universe_wsgi.ini' or set
up a sym link.


I hope this helps/clarifies

Regards, Hans-Rudolf






On 06/04/2014 04:49 AM, neil.burd...@csiro.au wrote:

Hi,
  we have the default setup for galaxy hence using SQLite database
and all data store in the same location as the galaxy install.

In Universe_wsgi.ini file there is an entry

# Dataset files are stored in this directory.
#file_path = database/files

How do we go about moving the database to a new location? We don't
really want to delete the data already present in the database just move
it to a new location. If we modify file_path and restart wouldn't that
cause further problems as some data would be in one location and other
in another location. Is it even possible to move the database once it
has been created and has data in it?

Thanks

Neil


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[galaxy-dev] Fwd: Re: Move galaxy/database (SQLite) to a new location

[Hans-Rudolf Hotz]

oops - forget to keep it on the list


 Original Message 
Subject: Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location
Date: Wed, 04 Jun 2014 09:11:00 +0200
From: Hans-Rudolf Hotz 
To: neil.burd...@csiro.au

Hi Neil

First a little comment: I strongly suggest to switch over to PostgreSQL.

Keep in mind that the 'database' (in your case the SQLite database) does
not contain any data. The 'database' contains just the meta data and the
users data which is required to run Galaxy.

"#file_path = database/files" is the location where the data sets are
stored. You can copy the contents of "~/database/files/ to a new
location and make the appropriate changes in 'universe_wsgi.ini' or set
up a sym link.


I hope this helps/clarifies

Regards, Hans-Rudolf






On 06/04/2014 04:49 AM, neil.burd...@csiro.au wrote:

Hi,
 we have the default setup for galaxy hence using SQLite database
and all data store in the same location as the galaxy install.

In Universe_wsgi.ini file there is an entry

# Dataset files are stored in this directory.
#file_path = database/files

How do we go about moving the database to a new location? We don't
really want to delete the data already present in the database just move
it to a new location. If we modify file_path and restart wouldn't that
cause further problems as some data would be in one location and other
in another location. Is it even possible to move the database once it
has been created and has data in it?

Thanks

Neil


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[galaxy-dev] How to unsubscribe - was: Re: RFC: Citations for tools

[Hans-Rudolf Hotz]

Hi Shari

Have a look at the last few lines of the e-mail:

"... To manage your subscriptions to this
 and other Galaxy lists, please use the interface
 at: http://lists.bx.psu.edu/"



Hans-Rudolf


On 05/28/2014 03:56 AM, Shari Javadiyan wrote:

Hi all,
Is there any way to unsubscribes from mail lists?
Cheers,
Shari


On Wednesday, 28 May 2014 2:52 AM, Jim McCusker
 wrote:


I would suggest using as much as possible from PROV, especially since
other workflow engines (Taverna and Pegasus come to mind) already
support it. Rather than looking for bibtex mappings in XML, we should be
looking for vocabularies that represent the elements we need to
represent, and the relevant bibtex should be generated from that. PROV
and Dublin Core Terms can get us most of the way there, I think.

Jim


On Tue, May 27, 2014 at 1:09 PM, Peter Cock mailto:p.j.a.c...@googlemail.com>> wrote:

Hi Eric,

I was sure there was a Trello card for this, but I can't find it
right now...

I've pushed this idea on the mailing list before, and in person at
the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html

Are you familiar enough with the area of semantic web/linked
data to know what would be the best XML based markup to
use for embedding the citations?

i.e. We should not reinvent the wheel here ;)

Peter


On Tue, May 27, 2014 at 5:54 PM, James Taylor mailto:ja...@jamestaylor.org>> wrote:
 > Eric, I'm very much in favor of this feature, and particularly the
 > idea of generating a list of citations from a history or workflow. I
 > imagine the only thing to quibble about will be the syntax. There are
 > already some efforts to represent bibtex in xml (e.g.
 > https://github.com/Zearin/BibTeXML), however they have always struck
 > me as overly verbose.
 >
 > -- jt
 >
 >
 > On Tue, May 27, 2014 at 12:45 PM, Eric Rasche
mailto:rasche.e...@yandex.ru>> wrote:
 >> -BEGIN PGP SIGNED MESSAGE-
 >> Hash: SHA1
 >>
 >> I'd want to open up discussion on a feature I'd like to see.
I'll try
 >> and implement it if I can find time this summer. I didn't see a
trello
 >> card for anything like this yet, but please feel free to direct
me there
 >> if I missed it.
 >>
 >>
 >> I'd like to see citations as a part of every tool.
 >>
 >> This would happen in the form of a  block in the XML,
which
 >> would contain sub-elements with text. These sub-elements could
be based
 >> off of BibTeX, since they have existing specs for citing things:
 >> https://en.wikipedia.org/wiki/BibTeX
 >>
 >> These citations would then be accessible in the HTML generated tool
 >> pages, or via a View/Download button somewhere on the tool page. By
 >> storing as an XML tree, we could render these citations as BibTeX
 >> entries for the LaTeX users, and I believe there are ways to convert
 >> BibTeX to EndNote XML and so on.
 >>
 >> This could be extended for use in workflows so that when you run
 >> workflows, somehow a list of citations for all tools used could be
 >> generated.
 >>
 >> Anyone have thoughts or opinions on this?
 >>
 >>
 >>
 >>
 >> Using the example bibtex entry from the wikipedia page:
 >>
 >> @Book{abramowitz+stegun,
 >>  author= "Milton {Abramowitz} and Irene A. {Stegun}",
 >>  title = "Handbook of Mathematical Functions with
 >>   Formulas, Graphs, and Mathematical Tables",
 >>  publisher = "Dover",
 >>  year  =  1964,
 >>  address   = "New York",
 >>  edition   = "ninth Dover printing, tenth GPO printing"
 >> }
 >>
 >> I imagine it'd look like the following in a real-life tool:
 >>
 >> 
 >>   ...
 >>   
 >> Milton Abramowitz and Irene A. Stegun"
 >> Handbook of Mathematical Functions with Formulas,
Graphs, and
 >> Mathematical Tables
 >> Dover
 >> 1964
 >> New York
 >> ninth Dover printing, tenth GPO printing
 >>   
 >> 
 >>
 >>
 >> Cheers,
 >> Eric
 >> - --
 >> Eric Rasche
 >> Programmer II
 >> Center for Phage Technology
 >> Texas A&M University
 >> College Station, TX 77843
 >> 404-692-2048
 >> e...@tamu.edu 
 >> rasche.e...@yandex.ru 
 >> -BEGIN PGP SIGNATURE-
 >> Version: GnuPG v2.0.17 (GNU/Linux)
 >>
 >> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
 >> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
 >> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
 >> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgi

Re: [galaxy-dev] Galaxy queue

[Hans-Rudolf Hotz]

On 05/26/2014 10:00 AM, Peter Cock wrote:

Hi Neil,

Via the GUI, if you are logged in as an administrator
(i.e. your email address is listed in universe_wsgi.ini)
there is a an admin tab (top banner, starting analyze
data etc). This includes an option to see the current jobs.

Via the command line API? I'm not sure, never looked.



connect to the PostgreSQL (or MySQL) database - prferably with a 
read-only user, and count the jobs with state "new" (ie grey) and 
"running" (ie yellow) in the "job" table. And based on the other 
information stored in the "job" table (eg 'tool_id'), you can make a 
guess on the expected wait time


Regards, Hans-Rudolf






Peter

On Mon, May 26, 2014 at 6:59 AM,   wrote:

Hi,
is there anyway to find out (from the command line or api) what is on the
Galaxy queue?

When items are queued they appear in grey or processing in yellow can I get
hold of these details from the command line as I could then email the user
who has just submitted a job with his place on queue and expected wait time.

Thanks
Neil

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Re: [galaxy-dev] user specific access/options

[Hans-Rudolf Hotz]

Hi Emma

Have a look at

https://wiki.galaxyproject.org/Admin/Config/Access%20Control
and
https://wiki.galaxyproject.org/UserDefinedToolboxFilters


as an alternative you could also do a bad hack using  "dynamic_options"


Regards, Hans-Rudolf



On 05/19/2014 10:38 AM, Emma Prudent wrote:

Hi,

I am currently an intern and I work on galaxy, particularly on this
acces problem.
So I am very interested in the answers that could be given to this question.

Thanks to you,

Emma Prudent

Hi Petr,

I am going to forward your email to the galaxy-dev list so that the
development community can offer comments/suggestions.

Best,

Jen
Galaxy team

On 8/30/11 2:27 AM, Petr Novak wrote:

/  Hi everybody,

/>/  I am developing the application on Galaxy server. One of the requirement
/>/  is to create user specific list of options. Is it possible to access
/>/  somehow $__user_email__  in  tag  or in  ?. I did
/>/  not found documentation how to used cheetah in galaxy tool xml files but
/>/  from files provided with galaxy, cheetah is used only in  and
/>/   tag. Is that rigth? If it can be used in any part of xml
/>/  definition file it would make much easier to generate xml dynamicaly
/>/  based on the $__user_email__
/>/  Does anybody have an idea how to manage this problem?
/>/  Petr Novak/



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Re: [galaxy-dev] Conditional parameters don't work with radio display

[Hans-Rudolf Hotz]

Hi Peter

yes, we have been running into the same problem and it is an old problem 
which has been reported long time ago by other people as well, eg:
Pieter Neerincx' email from May  2010 (Conditional params don't update 
properly when using radio buttons instead of popup menus.):


I found the email in this thread:
http://dev.list.galaxyproject.org/Galaxy-with-non-SGE-non-Torque-distributed-jobs-tt4136865.html#a4136880


I guess this was reported before Trello was in use and the issue was lost?


Hans-Rudolf



On 05/15/2014 03:37 PM, Peter Cock wrote:

Hello all,

I ran into a problem with a conditional select parameter not working when
shown as a radio box - despite the HTML having refresh_on_change set:

 
 Molecule type of FASTA inputs:
 protein
nucleotide
 
 

The simple workaround of using a drop-box select box instead worked, e.g.
https://github.com/peterjc/galaxy_blast/commit/f70245e25ce171e1508585baea19688cab4786e5

Is this something anyone else has noticed? Should I file an issue?

Thanks,

Peter

--

This is what I was testing with initially,

$ hg branch
default

$ hg log -b default | head
changeset:   13855:215f23b27be9
tag: tip
user:Carl Eberhard 
date:Tue Mar 18 16:14:52 2014 -0400
summary: Page-embedded histories: allow embedding the same history
more than once by removing the reliance on DOM ids and
selecting/traversing based on sibling relation of the history's script

I updated, same problem:

$ hg log -b default | head
changeset:   14501:75be6c49a65d
tag: tip
user:guerler
date:Wed May 14 22:49:44 2014 -0400
summary: Charts: Fix style
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Re: [galaxy-dev] reports page download

[Hans-Rudolf Hotz]

Hi Neil

I am not aware of any (hidden) download options.

I usually go with 'copy-paste' and process in R or manually. Also, if I 
need specific information which is often not displayed on the reports 
page I get it directly out of the MySQL/PostgreSQL database. For such 
cases it is handy to have a read-only user (just to make sure you don't 
do something bad by accident)


Hans-Rudolf


On 05/15/2014 08:07 AM, neil.burd...@csiro.au wrote:

Hi,
is there a way to download the information found on the reports page
so it can be used in excel for example?

Thanks
Neil


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Re: [galaxy-dev] Manual Tool and dependency installation

[Hans-Rudolf Hotz]

Hi Ravi


To start, have a look at those wiki pages:

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

Regards, Hans-Rudolf



On 05/14/2014 06:43 PM, Ravi Alla wrote:

Hi All,
Due to the nature of our cluster we are not allowed to have compilers on our 
webserver, which is where our galaxy instance runs. Because of this tool 
dependencies and tools that need to be compiled fail to install through the 
galaxy tool shed webpage. Is there a way for me to install dependencies and 
tools manually? For example I am trying to install the GATK2 wrapper. This 
depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is 
there instructions somewhere as to where to install these tools such that they 
are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am 
really out of sorts here.
Thank you
Ravi
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Re: [galaxy-dev] Taking backups of my galaxy instance

[Hans-Rudolf Hotz]

Hi Nilaksha

I don't really understand your question, but a simple answer is:

Make a backup of the complete galaxy directory tree and make a backup of 
your PostgreSQL database. You should do this anyway on a regularly 
basis, if you use your Galaxy server in production. Since much more 
likely, you will run into a storage failure, than experiencing "galaxy 
stop responding".


Regards, Hans-Rudolf


On 05/09/2014 06:52 AM, Nilaksha Neththikumara wrote:

Hi all,

I have installed and currently running a local galaxy instance
successfully, customized with desired tools and datasets but suddenly
got realized what would I do if anything goes wrong and galaxy stop
responding :O. Is there a specific way to take backups of a locally
installed galaxy instance with its own settings, so i can perform that
task regularly.
Thanks in advance :)

Sincerely,
Nilaksha.


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Re: [galaxy-dev] xml file display problem

[Hans-Rudolf Hotz]

Hi John

Thank you very much for the explanation. I will discuss it with our 
sys-admin


Hans-Rudolf

On 05/08/2014 03:29 PM, John Chilton wrote:

I broke your Galaxy and did so intentionally - I feel bad about that.
The way Galaxy was serving out XML content allowed XSS attacks between
users - 
http://dev.list.galaxyproject.org/using-svg-foreignObject-tags-can-circumvent-html-sanitization-td4663390.html.

If you aren't running a public instance, one could just set
serve_xss_vulnerable_mimetypes to True in your universe_wsgi.ini file
to disable the changed behavior. There are some relevant Trello cards
referenced in that e-mail for longer term fixes more appropriate for
public servers or servers where you don't or cannot trust your users.

-John

On Thu, May 8, 2014 at 7:39 AM, Hans-Rudolf Hotz  wrote:

Hi

This is long shot, but maybe someone can help us


We are in the process of upgrading our production galaxy server from
("release_2013.11.04" to "release_2014.04.14"). Despite some "hiccups" it
went very smooth (I might come back with those in a different mail thread
next week). However, we are running into a display problem:


A former co-worker has written a tool which generates a big xml file. When
clicking on the 'eye' icon, we don't wan't display the complete file, but
only part of it. For this he has written an xsl file ("qProject.xsl"). This
file is placed in ~/galaxy-dist/static/

Correspondingly, the beginning of the xml file looks like:



  
   etc.

And (at least for me by magic), when you now click on the 'eye' icon a
nicely formatted output was displayed, instead of the full xml file. This
has been the case with the "release_2013.11.04" distribution.

Now with the "release_2014.04.14" distribution (and also already with
"release_2014.02.10"), this magic trick does not work anymore, and the
complete, un-formatted xml file is displayed.

I am aware, there has been major changes introduced for the displays with
the "release_2014.02.10" distribution. So, can anybody give me some hints
how to get this working again. I am happy to provide more details, if
required.


Thank you very much
Hans-Rudolf






--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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[galaxy-dev] xml file display problem

[Hans-Rudolf Hotz]

Hi

This is long shot, but maybe someone can help us


We are in the process of upgrading our production galaxy server from 
("release_2013.11.04" to "release_2014.04.14"). Despite some "hiccups" 
it went very smooth (I might come back with those in a different mail 
thread next week). However, we are running into a display problem:



A former co-worker has written a tool which generates a big xml file. 
When clicking on the 'eye' icon, we don't wan't display the complete 
file, but only part of it. For this he has written an xsl file 
("qProject.xsl"). This file is placed in ~/galaxy-dist/static/


Correspondingly, the beginning of the xml file looks like:



 
  etc.

And (at least for me by magic), when you now click on the 'eye' icon a 
nicely formatted output was displayed, instead of the full xml file. 
This has been the case with the "release_2013.11.04" distribution.


Now with the "release_2014.04.14" distribution (and also already with 
"release_2014.02.10"), this magic trick does not work anymore, and the 
complete, un-formatted xml file is displayed.


I am aware, there has been major changes introduced for the displays 
with the "release_2014.02.10" distribution. So, can anybody give me some 
hints how to get this working again. I am happy to provide more details, 
if required.



Thank you very much
Hans-Rudolf






--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Galaxy Error Message

[Hans-Rudolf Hotz]

Hi Brad

To me, this looks like an error in tool definition file (ie the xml 
file). Something like using $gene in the "command" tag without defining 
it in a "param" tag. But it is difficult to guess without seeing to full 
xml file.



Regards Hans-Rudolf

On 04/29/2014 06:13 PM, Bradley Belfiore wrote:

Upon  going back over my script I got it working on the command line as
suggested, and when attempting to execute in my instance of galaxy I got
this error message which I was not sure about:

Traceback (most recent call last):
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 
152, in prepare_job
 job_wrapper.prepare()
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in 
prepare
 self.command_line = self.tool.build_command_line( param_dict )
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, 
in build_command_line
 command_line = fill_template( self.command, context=param_dict )
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in 
fill_template
 return str( Template( source=template_text, searchList=[context] ) )
   File 
"/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py",
 line 1004, in __str__
 return getattr(self, mainMethName)()
   File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
NotFound: cannot find 'gene'



On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Brad



On 04/28/2014 05:26 PM, Bradley Belfiore wrote:

So upon doing what you suggested, I get:

bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R
'/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA'


I said  "Rscript_wrapper.sh /Users/bbelfio1/galaxy-."

I don't see the word "Rscript_wrapper.sh" in your line, hence it
does not correspond to the command galaxy is executing

You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt',
'04110', and 'HSA'

However in an earlier mail you mention four arguments:
$genedata
$pathwayid
$species
$output

Error in grep(species, pathway.id <http://pathway.id>
<http://pathway.id>) :

argument "pathway.id <http://pathway.id>
<http://pathway.id>" is missing, with no default


Calls: pathview -> grep

Execution halted



As long as you are not sure, whether your script is working on the
command line the way you want it to be executed in Galaxy, there is
no point in putting it into Galaxy


  Hans-Rudolf




On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>
<mailto:h...@fmi.ch <mailto:h...@fmi.ch>>> wrote:

 This is not what I suggested, I said


 Rscript_wrapper.sh
 /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
$genedata

 $pathwayid $species $output

 replacing $genedata $pathwayid $species $output with meaningful
 arguments




 On 04/28/2014 04:29 PM, Bradley Belfiore wrote:

 Yes when running in command line I get:

 bravo:galaxy-dist bbelfio1$ Rscript
 /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R


 Error in value[[3L]](cond) :

 failed to read experimental design data: cannot
open the
 connection

 Calls: tryCatch -> tryCatchList -> tryCatchOne ->


 In addition: Warning message:

 In file(file, "rt") : cannot open file 'NA': No such
file or
 directory

 Execution halted



 On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock
 mailto:p.j.a.c...@googlemail.com>
<mailto:p.j.a.cock@googlemail.__com
<mailto:p.j.a.c...@googlemail.com>>
 <mailto:p.j.a.cock@googlemail.
<mailto:p.j.a.cock@googlemail.>com

 <mailto:p.j.a.cock@googlemail.__com
<mailto:p.j.a.c...@googlemail.com>>>> wrote:

   > On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
   >>
   >> The initial error now seems to be taken care
of and now am
  getting this
   >> message on attempting to run tool:
   >>
   >> File



"/Users/bbelfio1/galaxy-dist/lib

Re: [galaxy-dev] Galaxy Error Message

[Hans-Rudolf Hotz]

Hi Brad


On 04/28/2014 05:26 PM, Bradley Belfiore wrote:

So upon doing what you suggested, I get:

bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
'/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA'



I said  "Rscript_wrapper.sh /Users/bbelfio1/galaxy-."

I don't see the word "Rscript_wrapper.sh" in your line, hence it does 
not correspond to the command galaxy is executing


You provide 3 arguments '/Users/bbelfio1/Documents/sample.txt', '04110', 
and 'HSA'


However in an earlier mail you mention four arguments:
$genedata
$pathwayid
$species
$output


Error in grep(species, pathway.id <http://pathway.id>) :

   argument "pathway.id <http://pathway.id>" is missing, with no default

Calls: pathview -> grep

Execution halted




As long as you are not sure, whether your script is working on the 
command line the way you want it to be executed in Galaxy, there is no 
point in putting it into Galaxy



 Hans-Rudolf





On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

This is not what I suggested, I said


Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata
$pathwayid $species $output

replacing $genedata $pathwayid $species $output with meaningful
arguments




On 04/28/2014 04:29 PM, Bradley Belfiore wrote:

Yes when running in command line I get:

bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R

Error in value[[3L]](cond) :

failed to read experimental design data: cannot open the
connection

Calls: tryCatch -> tryCatchList -> tryCatchOne -> 

In addition: Warning message:

In file(file, "rt") : cannot open file 'NA': No such file or
directory

Execution halted



On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock
mailto:p.j.a.c...@googlemail.com>
<mailto:p.j.a.cock@googlemail.__com
<mailto:p.j.a.c...@googlemail.com>>> wrote:

  > On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
  >>
  >> The initial error now seems to be taken care of and now am
 getting this
  >> message on attempting to run tool:
  >>
  >> File

"/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/runners/init__.py",
  >> line 153, in prepare_job
  >>  job_wrapper.runner_command___line =
self.build_command_line(
  >> job_wrapper, include_metadata=include___metadata,
  >> include_work_dir_outputs=__include_work_dir_outputs )
  >>File

"/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/runners/init__.py",
  >> line 176, in build_command_line
  >>  return build_command( self, job_wrapper,
  >> include_metadata=include___metadata,
  >> include_work_dir_outputs=__include_work_dir_outputs )
  >>File

"/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/command___factory.py",
  >> line 19, in build_command
  >>  commands_builder =
 CommandsBuilder(job_wrapper.__get_command_line())
  >>File

"/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/command___factory.py",
  >> line 109, in __init__
  >>  commands = initial_command.rstrip("; ")
  >> AttributeError: 'NoneType' object has no attribute 'rstrip'
  >>

 This is still breaking inside Galaxy, before ever trying to
run your
 scripts. There is likely still a problem in your XML.

 On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz
mailto:h...@fmi.ch>
 <mailto:h...@fmi.ch <mailto:h...@fmi.ch>>> wrote:
  > again, have you tried running your Rscript outside of Galaxy
 called by
  > Rscript_wrapper.sh ?
  >

 This is an important question :)

 Also, please remember to CC the mailing list and not just reply
 to the previous email's sender only.

 Thanks,

 Peter




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Re: [galaxy-dev] Galaxy Error Message

[Hans-Rudolf Hotz]

This is not what I suggested, I said

Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata 
$pathwayid $species $output


replacing $genedata $pathwayid $species $output with meaningful arguments




On 04/28/2014 04:29 PM, Bradley Belfiore wrote:

Yes when running in command line I get:

bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R

Error in value[[3L]](cond) :

   failed to read experimental design data: cannot open the connection

Calls: tryCatch -> tryCatchList -> tryCatchOne -> 

In addition: Warning message:

In file(file, "rt") : cannot open file 'NA': No such file or directory

Execution halted



On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock mailto:p.j.a.c...@googlemail.com>> wrote:

 > On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
 >>
 >> The initial error now seems to be taken care of and now am
getting this
 >> message on attempting to run tool:
 >>
 >> File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
 >> line 153, in prepare_job
 >>  job_wrapper.runner_command_line = self.build_command_line(
 >> job_wrapper, include_metadata=include_metadata,
 >> include_work_dir_outputs=include_work_dir_outputs )
 >>File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
 >> line 176, in build_command_line
 >>  return build_command( self, job_wrapper,
 >> include_metadata=include_metadata,
 >> include_work_dir_outputs=include_work_dir_outputs )
 >>File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
 >> line 19, in build_command
 >>  commands_builder =
CommandsBuilder(job_wrapper.get_command_line())
 >>File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
 >> line 109, in __init__
 >>  commands = initial_command.rstrip("; ")
 >> AttributeError: 'NoneType' object has no attribute 'rstrip'
 >>

This is still breaking inside Galaxy, before ever trying to run your
scripts. There is likely still a problem in your XML.

On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:
 > again, have you tried running your Rscript outside of Galaxy
called by
 > Rscript_wrapper.sh ?
 >

This is an important question :)

Also, please remember to CC the mailing list and not just reply
to the previous email's sender only.

Thanks,

Peter



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Re: [galaxy-dev] Galaxy Error Message

[Hans-Rudolf Hotz]

again, have you tried running your Rscript outside of Galaxy called by 
Rscript_wrapper.sh ?


To me, it looks like you have a bug in your Rscript and/or your wrapper.


Hans-Rudolf


On 04/28/2014 03:58 PM, Bradley Belfiore wrote:

The initial error now seems to be taken care of and now am getting this
message on attempting to run tool:

File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 
153, in prepare_job
 job_wrapper.runner_command_line = self.build_command_line( job_wrapper, 
include_metadata=include_metadata, 
include_work_dir_outputs=include_work_dir_outputs )
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 
176, in build_command_line
 return build_command( self, job_wrapper, 
include_metadata=include_metadata, 
include_work_dir_outputs=include_work_dir_outputs )
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 
19, in build_command
 commands_builder = CommandsBuilder(job_wrapper.get_command_line())
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 
109, in __init__
 commands = initial_command.rstrip("; ")
AttributeError: 'NoneType' object has no attribute 'rstrip'



On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

"Please keep all replies on the list by using "reply all""


well, what happens if you run


Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata
$pathwayid $species $output

on the command line yourself (or rather as the user galaxy is
running as), replacing $genedata $pathwayid $species $output with
meaningful arguments


Hans-Rudolf





On 04/28/2014 03:32 PM, Bradley Belfiore wrote:

Thank you for your quick response, my command tag is:

interpreter="bash">Rscript___wrapper.sh
/Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata
$pathwayid $species $output


So I believe Im calling R via the Rscript_wrapper.sh?

As far as the #!/bin/bash, not sure why I had that there, I took
    it out now.
thanks,
Bradley Belfiore


On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>
<mailto:h...@fmi.ch <mailto:h...@fmi.ch>>> wrote:

 Hi Brad

 I don't you are using R to execute your R script

 How do you call your R script, ie how does the command tag
looks in
 the tool definition file?

 Also, why do you have a "#!/bin/bash" at the beginning of
your R script?


 Regards, Hans-Rudolf




 On 04/27/2014 09:50 PM, Bradley Belfiore wrote:

 I am new to galaxy and while trying to convert an R
tool to a Galaxy
 usable tool I keep  getting:

/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1:

 syntax
 error near unexpected token `('


/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1:

 `args=(commandArgs(TRUE))'


 any help as to how to remedy this would be greatly
appreciated.  The
 first couple lines of my .R file are
 #
 #!/bin/bash
 args<-(commandArgs(TRUE))

 Thanks,
 Brad



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<http://galaxyproject.org/__search/mailinglists/>
 <http://galaxyproject.org/__search/mailinglists/
<http://galaxyproject.org/search/mailinglists/>>




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Re: [galaxy-dev] Galaxy Error Message

[Hans-Rudolf Hotz]

"Please keep all replies on the list by using "reply all""


well, what happens if you run

Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata 
$pathwayid $species $output


on the command line yourself (or rather as the user galaxy is running 
as), replacing $genedata $pathwayid $species $output with meaningful 
arguments



Hans-Rudolf




On 04/28/2014 03:32 PM, Bradley Belfiore wrote:

Thank you for your quick response, my command tag is:

interpreter="bash">Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output


So I believe Im calling R via the Rscript_wrapper.sh?

As far as the #!/bin/bash, not sure why I had that there, I took it out now.
thanks,
Bradley Belfiore


On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Brad

I don't you are using R to execute your R script

How do you call your R script, ie how does the command tag looks in
the tool definition file?

Also, why do you have a "#!/bin/bash" at the beginning of your R script?


Regards, Hans-Rudolf




On 04/27/2014 09:50 PM, Bradley Belfiore wrote:

I am new to galaxy and while trying to convert an R tool to a Galaxy
usable tool I keep  getting:
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
syntax
error near unexpected token `('

/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'


any help as to how to remedy this would be greatly appreciated.  The
first couple lines of my .R file are
#
#!/bin/bash
args<-(commandArgs(TRUE))

Thanks,
Brad


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Re: [galaxy-dev] Galaxy Error Message

[Hans-Rudolf Hotz]

Hi Brad

I don't you are using R to execute your R script

How do you call your R script, ie how does the command tag looks in the 
tool definition file?


Also, why do you have a "#!/bin/bash" at the beginning of your R script?


Regards, Hans-Rudolf



On 04/27/2014 09:50 PM, Bradley Belfiore wrote:

I am new to galaxy and while trying to convert an R tool to a Galaxy
usable tool I keep  getting:
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: syntax
error near unexpected token `('

/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: 
`args=(commandArgs(TRUE))'


any help as to how to remedy this would be greatly appreciated.  The
first couple lines of my .R file are
#
#!/bin/bash
args<-(commandArgs(TRUE))

Thanks,
Brad


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Re: [galaxy-dev] automatically adding fasta files to "built-in" databases and selecting files questions

[Hans-Rudolf Hotz]

Hi Nik

Have a look at the "Profile Annotations" tool
(~/tools/annotation_profiler/annotation_profiler.xml)

and the file ~/tool-data/annotation_profiler_options.xml


Regards, Hans-Rudolf




On 04/19/2014 12:48 AM, Nikhil Joshi wrote:

Hi Hans,

Thanks for your response. I am trying to get just one part working right
now, and that is the selecting of a database file. You suggest using a
drill_down, but I can't seem to find good documentation on how to get it
to work. I have been looking at the annotation_profiler tool to get
ideas, but it still is unclear to me. Can you give me a simple example
of how one would create the file that the drill_down would use and then
how to use that file?

- Nik.



On Wed, Apr 9, 2014 at 1:13 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Nik

I don't think there is a solution out of the box for all of this,
but I will try to give you some pointers - others might have
different or even better suggestions (my suggestion are very
'hacky'). Let me answer your questions in reverse order:

- Instead of using "Add another file", display all your files as
   checkboxes:

   type="select" display="checkboxes" multiple="true"

   you then get a comma separated string with containing all the
   selected files

   one option to populate the checkboxes is using "dynamic_options" or
   "from_file" which both allow you to read the list of files stored in
a extra table


- A list with thousands of files to choose from is obviously not very
   handy. You can build a tree where you can open and collapse
   individual branches using

   type="drill_down" together with "from_file"

   Or as an alternative to searching, you can use "conditional" and then
   only display part of the list.


- you can write a little tool, which allows people to select a
   history item (or uploads a new file) which is then stored at a new
   location (outside the galaxy database directory). In a second step,
   this tool adds the item to the table which is read by
   "dynamic_options" or "from_file". Using "from_file" would require a
   restart, but a tool reload.


I hope you get a few ideas out of this

Regards, Hans-Rudolf




On 04/09/2014 04:34 AM, Nikhil Joshi wrote:

Hi all,

We have a local install of Galaxy that we use for testing for our
bioinformatics courses. I am creating some new tool interfaces
for the
install. I want to create a tool that will allow a user to
automatically
add a fasta database to the "built-in" databases (without needing to
reboot the server). Is this possible?

Along with that issue is that the number of databases for this
tool can
number in the thousands. Is there a way to easily search the
built-in
databases for the database you are looking for, and then use that
database in a tool? Right now, it is an enormous drop down list
which is
really annoying and unwieldy.

Finally, these tools can take multiple input files, but I really
don't
like the way galaxy handles that where you have to continually
click on
"Add another file". Is there a method or work-around in galaxy
where you
can have a multi-file select?

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.__edu/
<http://bioinformatics.ucdavis.edu/>
najoshi -at- ucdavis -dot- edu
530.752.2698  (w)


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--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

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Re: [galaxy-dev] Migrate user data to a new server

[Hans-Rudolf Hotz]

Hi Simon

I recommend the following (minimal) steps to migrate to a new server:

 - set up the new server using the SAME Galaxy version your old server
   is running.

 - copy the contents of the 'database' directory

 - make the site specific adjustment, e.g. universe_wsgi.ini

 - connect your new server to your existing PostgreSQL database

 - and start your new server, followed by an upgrade to the new Galaxy
   version


Of course, there are many other points to take care of like the existing 
data libraries and other site specific changes only you know about. 
Hence I recommend to first work with a copy of your PostgreSQL database, 
test everything, and then make an rsync of the 'database' directory and 
switch to the real PostgreSQL database. This way, your user can continue 
working with the old server, while you test the new one.



I hope this gives you a few ideas
Regards, Hans-Rudolf


On 04/15/2014 06:00 AM, Simon Gladman wrote:

Hi all,

I've tried looking in the mailing list for this to no avail. (Maybe my
search terms were no good..)

I administer a server with about 15 users. The server is failing and so
I have set up a new server (with an updated OS, Galaxy version etc
(galaxy versions: old - nov 2013, new - Feb 2014). Is there a method for
migrating my users and their data across to the new server, without
getting them to tell me their passwords

Cheers,

Simon.


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Re: [galaxy-dev] automatically adding fasta files to "built-in" databases and selecting files questions

[Hans-Rudolf Hotz]

Hi Nik

I don't think there is a solution out of the box for all of this, but I 
will try to give you some pointers - others might have different or even 
better suggestions (my suggestion are very 'hacky'). Let me answer your 
questions in reverse order:


- Instead of using "Add another file", display all your files as
  checkboxes:

  type="select" display="checkboxes" multiple="true"

  you then get a comma separated string with containing all the
  selected files

  one option to populate the checkboxes is using "dynamic_options" or
  "from_file" which both allow you to read the list of files stored in
   a extra table


- A list with thousands of files to choose from is obviously not very
  handy. You can build a tree where you can open and collapse
  individual branches using

  type="drill_down" together with "from_file"

  Or as an alternative to searching, you can use "conditional" and then
  only display part of the list.


- you can write a little tool, which allows people to select a
  history item (or uploads a new file) which is then stored at a new
  location (outside the galaxy database directory). In a second step,
  this tool adds the item to the table which is read by
  "dynamic_options" or "from_file". Using "from_file" would require a
  restart, but a tool reload.


I hope you get a few ideas out of this

Regards, Hans-Rudolf



On 04/09/2014 04:34 AM, Nikhil Joshi wrote:

Hi all,

We have a local install of Galaxy that we use for testing for our
bioinformatics courses. I am creating some new tool interfaces for the
install. I want to create a tool that will allow a user to automatically
add a fasta database to the "built-in" databases (without needing to
reboot the server). Is this possible?

Along with that issue is that the number of databases for this tool can
number in the thousands. Is there a way to easily search the built-in
databases for the database you are looking for, and then use that
database in a tool? Right now, it is an enormous drop down list which is
really annoying and unwieldy.

Finally, these tools can take multiple input files, but I really don't
like the way galaxy handles that where you have to continually click on
"Add another file". Is there a method or work-around in galaxy where you
can have a multi-file select?

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)


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Re: [galaxy-dev] visualization button

[Hans-Rudolf Hotz]

Philip

Using a the first column as label should work if you tick the box 
"Include a third column as data point IDs?"


Regards, Hans-Rudolf


On 04/09/2014 07:47 AM, Philippe Moncuquet wrote:

Hi Hans-Rudolph,

Ok so the syntax in the wrapper was not the problem. My file was tabular
but the first column contained string and numbers whereas the second
column contained only numbers. When I added a 3rd column with numbers to
test I was able to see the button and generate some graphics. I wish It
could have taken the first column as the label for the second but I
understand that would produces unwanted behavior in other context.
Anyway, all good, thanks for the help.

Regards,
Philip


2014-04-08 17:33 GMT+10:00 Hans-Rudolf Hotz mailto:h...@fmi.ch>>:



On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:

Hi Rudolph,

Thanks for the answer. I understand that it would make no sense
to allow
generation of graphics on non relevant data. My data is in tabular
format and that is the reason why I was surprise not to see that
button.


  



I would re-write this like:


   



Also, make sure your output is actually a table, ie it does consist
of more than one (tab-separated) column.


Hans-Rudolf


I wouldn't be surprised if something was wrong in my syntax.
Thanks for
the help anyway.

Cheers,
Philip


2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz mailto:h...@fmi.ch>
<mailto:h...@fmi.ch <mailto:h...@fmi.ch>>>:


 Hi Philip

 The appearance of the visualization button depends on the
datatype
 of your output. E.g. when it is set to 'tabular', you
should get the
 button allowing you to create a scatter plot.

 However, depending on your data, it might not make much
sense to
 visualize it in 'Trackster', 'Circster' or as scatter plot.


 Regards, Hans-Rudolf



 On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:

 Hi,

 I have developed a simple script that give some
statistics on an
 assemble. It generates a tabular output. The visualization
 button is not
 available when I extend the output in the history pane.
Is there any
 code that I need to put in my xml wrapper to get this
button
 available ?

 Regards,
 Philip



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 <http://galaxyproject.org/__search/mailinglists/
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Re: [galaxy-dev] visualization button

[Hans-Rudolf Hotz]

On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:

Hi Rudolph,

Thanks for the answer. I understand that it would make no sense to allow
generation of graphics on non relevant data. My data is in tabular
format and that is the reason why I was surprise not to see that button.

   
 
   



I would re-write this like:


  



Also, make sure your output is actually a table, ie it does consist of 
more than one (tab-separated) column.



Hans-Rudolf



I wouldn't be surprised if something was wrong in my syntax. Thanks for
the help anyway.

Cheers,
Philip


2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz mailto:h...@fmi.ch>>:

Hi Philip

The appearance of the visualization button depends on the datatype
of your output. E.g. when it is set to 'tabular', you should get the
button allowing you to create a scatter plot.

However, depending on your data, it might not make much sense to
visualize it in 'Trackster', 'Circster' or as scatter plot.


Regards, Hans-Rudolf



On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:

Hi,

I have developed a simple script that give some statistics on an
assemble. It generates a tabular output. The visualization
button is not
available when I extend the output in the history pane. Is there any
code that I need to put in my xml wrapper to get this button
available ?

Regards,
Philip


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Re: [galaxy-dev] visualization button

[Hans-Rudolf Hotz]

Hi Philip

The appearance of the visualization button depends on the datatype of 
your output. E.g. when it is set to 'tabular', you should get the button 
allowing you to create a scatter plot.


However, depending on your data, it might not make much sense to 
visualize it in 'Trackster', 'Circster' or as scatter plot.



Regards, Hans-Rudolf


On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:

Hi,

I have developed a simple script that give some statistics on an
assemble. It generates a tabular output. The visualization button is not
available when I extend the output in the history pane. Is there any
code that I need to put in my xml wrapper to get this button available ?

Regards,
Philip


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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

[Hans-Rudolf Hotz]

This might be due to different version of Galaxy. Is the "Job 
Command-Line" listed? - Depending on the tool, you might find the path 
there.


Hans-Rudolf



:Do you have the will also find the path in the "job command

On 04/03/2014 09:03 AM, Nilaksha Neththikumara wrote:

Hi,
Thanks a lot for the answer. But I'm afraid that detail panel does not
give me the path to the dataset. Have you encountered this problem before?

Nilaksha


On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Nilaksha

Use the "!" icon (View details) to get the full path to the data
set, and the use 'cp' or 'scp' (if not on the same host) on your
terminal.


Hope this helps, Hans-Rudolf



On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:

Hello all,

I'm currently successfully running a pipeline for metagenomic
analysis
on my locally installed galaxy instance and everything seemed to
good by
far. But when I'm trying to download my processed blast xml
output (I
used blast+ wrappers for this) , by clicking the small disk button
nothing happens. I tried several options.
1) clicked the 'disk' icon to initiate the downloading
2) right clicked the 'disk' icon and tried to use saved linked
as, but a
dialog box doesnot appear for saving
3) tried copying the link and used curl on bash terminal, but
progress
bar is stuck at 0%.

I think this is happening because my blast output dataset is
much larger
(around ~10GB) , but if that's the case, how am I supposed to
get the
data out of galaxy any way??

Thank a lot in advance.

Regards!
Nilaksha


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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

[Hans-Rudolf Hotz]

Hi Nilaksha

Use the "!" icon (View details) to get the full path to the data set, 
and the use 'cp' or 'scp' (if not on the same host) on your terminal.



Hope this helps, Hans-Rudolf


On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:

Hello all,

I'm currently successfully running a pipeline for metagenomic analysis
on my locally installed galaxy instance and everything seemed to good by
far. But when I'm trying to download my processed blast xml output (I
used blast+ wrappers for this) , by clicking the small disk button
nothing happens. I tried several options.
1) clicked the 'disk' icon to initiate the downloading
2) right clicked the 'disk' icon and tried to use saved linked as, but a
dialog box doesnot appear for saving
3) tried copying the link and used curl on bash terminal, but progress
bar is stuck at 0%.

I think this is happening because my blast output dataset is much larger
(around ~10GB) , but if that's the case, how am I supposed to get the
data out of galaxy any way??

Thank a lot in advance.

Regards!
Nilaksha


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Re: [galaxy-dev] Question concerning the xml file for local tools with multiple output files.

[Hans-Rudolf Hotz]

Hi Lifeng

I am glad to hear it works 

WRT your thoughts about using a wrapper script for each tool: I agree it might 
help you to standardize your tools, however it also introduces an extra step, 
which needs to be taken care of if  you want to change/upgrade your tool. 
Personally, I would only use a wrapper if it is necessary or it adds some 
benefits for the tool.  Others on the list might have a different opinion?

Hans-Rudolf



On Mar 25, 2014, at 3:13 PM, Lifeng Lin wrote:

> works like a charm. Thank you!
> I start to wonder if i should use this wrapper approach on all scripts 
> regardless of the original input-output format for standardized integration, 
> and possible automated integrations in the future.
> 
> 
> On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz  
> wrote:
> Hi Lifeng
> 
> The easiest way to execute your script will be to provide a wrapper script 
> (written in your preferred language, eg Python, perl, etc). Call the wrapper 
> script like this:
> 
> wrapper $input $output1 $output2
> 
> and define $output1 $output2 according to your needs: format="fasta", 
> format="txt"
> 
> 
> the wrapper will call your script and rename/move the output.
> 
> 
> Hope this helps,
> Regards, Hans-Rudolf
> 
> 
> On Mar 25, 2014, at 3:23 AM,  
>  wrote:
> 
> >
> > From: Lifeng Lin 
> > Date: March 25, 2014 12:58:52 AM GMT+01:00
> > To: 
> > Subject: Question concerning the xml file for local tools with multiple 
> > output files.
> >
> >
> > Hi folks,
> >
> > I am trying to integrate some of my local Perl scripts into a downloaded 
> > instance of Galaxy. So far the script with a simple "in_file to out_file" 
> > format worked great, but I am having problems understanding how to treat 
> > scripts with multiple output files that share the same input argv.
> > for example: the script run like this in command line:
> >
> > 

Re: [galaxy-dev] Question concerning the xml file for local tools with multiple output files.

[Hans-Rudolf Hotz]

Hi Lifeng

The easiest way to execute your script will be to provide a wrapper script 
(written in your preferred language, eg Python, perl, etc). Call the wrapper 
script like this:

wrapper $input $output1 $output2

and define $output1 $output2 according to your needs: format="fasta", 
format="txt"


the wrapper will call your script and rename/move the output.


Hope this helps, 
Regards, Hans-Rudolf


On Mar 25, 2014, at 3:23 AM,  
 wrote:

> 
> From: Lifeng Lin 
> Date: March 25, 2014 12:58:52 AM GMT+01:00
> To: 
> Subject: Question concerning the xml file for local tools with multiple 
> output files.
> 
> 
> Hi folks,
> 
> I am trying to integrate some of my local Perl scripts into a downloaded 
> instance of Galaxy. So far the script with a simple "in_file to out_file" 
> format worked great, but I am having problems understanding how to treat 
> scripts with multiple output files that share the same input argv.
> for example: the script run like this in command line:
> 
> 

Re: [galaxy-dev] Finding cruft in database/files/?

[Hans-Rudolf Hotz]

Hi Brian 

It is difficult to imagine where such files are coming from. As each file in 
~/database/files/*/ has a corresponding entry in the 'dataset' table.  If you 
have such files, then something went horribly wrong, eg by using two different 
databases on the same files system.  To double check manually compare the list 
of files on the file system, with the contents of the 'dataset' table.

Also, have a look at the ~/database/job_working_directory/ and ~/database/tmp/ 
directories. You might have some old, big files there using a lot of space.


Regards, Hans-Rudolf




On Mar 24, 2014, at 12:43 AM, Brian Claywell wrote:

> Daniel,
> 
> I've been using the purge scripts in cron jobs for a long time now;
> unless I missed something on that page, what I'm looking for is
> something slightly different -- rather than purging datasets marked as
> old/deleted/whatever in the Galaxy db, I want to find files that
> *aren't* in the Galaxy db but still exist on the filesystem.
> 
> On Sun, Mar 23, 2014 at 12:39 PM, Daniel Blankenberg  wrote:
>> Hi Brian,
>> 
>> Have a look at purging histories and datasets: 
>> https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
>> 
>> 
>> Thanks for using Galaxy,
>> 
>> Dan
>> 
>> On Mar 22, 2014, at 9:24 PM, Brian Claywell  wrote:
>> 
>>> Is there an existing method for finding files in
>>> $GALAXY_DIR/database/files that have been orphaned due to errors, or
>>> leftover from testing, etc? I'm pretty sure ours is bigger than it
>>> ought to be, and I'd really like to look at a little audit of the
>>> files there vs the ones registered in Galaxy.
>>> 
>>> Thanks!
>>> 
>>> --
>>> Brian Claywell, Systems Analyst/Programmer
>>> Fred Hutchinson Cancer Research Center
>>> bclay...@fhcrc.org
>>> ___
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>> 
> 
> 
> 
> -- 
> Brian Claywell, Systems Analyst/Programmer
> Fred Hutchinson Cancer Research Center
> bclay...@fhcrc.org
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Re: [galaxy-dev] can I change to PostgreSQL?

[Hans-Rudolf Hotz]

Have a look at 
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server


on how to set up the PostgreSQL database for Galaxy.

I am not aware of any tools to port the contents of the SQLite file to a 
PostgreSQL database, except for setting up an all new Galaxy server 
(running with PostgreSQL) and exporting the important histories from 
your old server followed by importing them into your new server - though 
looking at the size of your history, this might not work.



Hans-Rudolf

On 03/12/2014 09:57 AM, Milad Bastami wrote:

Many thanks for your help. Your are right about database (I'm using
SQLite). I've found a tutorial at GMOD
(http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work
with PostgreSQL, but can I change the current database to PostgreSQL
without missing my datasets? I am running a single-user galaxy instance.

Cheers, Milad


 > Date: Wed, 12 Mar 2014 09:07:00 +0100
 > From: h...@fmi.ch
 > To: mi.bast...@live.com
 > CC: galaxy-dev@lists.bx.psu.edu
 > Subject: Re: [galaxy-dev] error in workflow
 >
 > Hi Milad
 >
 > The error message: "database is locked" might be a hint.
 >
 > Are you using a PostgreSQL database or just SQLite ? If the latter, you
 > will often run in troubles when running more than one job at a time, due
 > to file locking.
 >
 > Regards, Hans-Rudolf
 >PostgreSQL
 >
 > On 03/11/2014 07:41 PM, Milad Bastami wrote:
 > > Dear Galaxy Developers,
 > > I'm running galaxy local on ubuntu and trying to run a workflow on
 > > multiple datasets (separately). Occasionally when I try to run workflow
 > > on input dataset I get "Unable to finish job" error in some steps, in
 > > most time the problem will be solved when I run the workflow again, but
 > > this going to happen more frequently. I attached the error message
here.
 > > I suspect it may be related to increase in number of datasets of the
 > > current history (1757 datasets with ~350GB size).
 > > I will appreciate your help
 > >
 > > Traceback (most recent call last):
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 116, in queue_job
 > > job_wrapper.finish( stdout, stderr, exit_code )
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 1068, in finish
 > > self.sa_session.flush()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
line 114, in do
 > > return getattr(self.registry(), name)(*args, **kwargs)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1718, in flush
 > > self._flush(objects)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1804, in _flush
 > > transaction.commit()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 365, in commit
 > > t[1].commit()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2045, in commit
 > > self._do_commit()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2075, in _do_commit
 > > self.connection._commit_impl()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1280, in _commit_impl
 > > self._handle_dbapi_exception(e, None, None, None, None)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1277, in _commit_impl
 > > self.engine.dialect.do_commit(self.connection)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 307, in do_commit
 > > connection.commit()
 > > OperationalError: (OperationalError) database is locked None None
 > >
 > >
 > >
 > > ___
 > > Please keep all replies on the list by using "reply all"
 > > in your mail client. To manage your subscriptions to this
 > > and other Galaxy lists, please use the interface at:
 > > http://lists.bx.psu.edu/
 > >
 > > To search Galaxy mailing lists use the unified search at:
 > > http://galaxyproject.org/search/mailinglists/
 > >

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 ht

Re: [galaxy-dev] History seems to load forever

[Hans-Rudolf Hotz]

Hi Carrie

Was the history which is causing troubles created before you switched to 
external authentication? Or has the user a slightly different e-mail 
address now? eg different use of capital letters, like 'foo.bar@home' 
and 'Foo.Bar@home'  - we had such problems, when we switched to external 
authentication.


I had to dig into our MySQL database and fix the "galaxy_user" table. In 
your case, I recommend looking at the "galaxy_user" table and check 
whether the user has more than one entry. Take the "id" (ie the number) 
and search the "history" table using the id as 'user_id'. I would guess 
you can fix your problem by changing the 'user_id' in the "history" 
table for the history which is causing troubles.


BUT, BE VERY CAREFUL! you can do a lot of damage to the database. Switch 
off the galaxy server first, and MAKE a back up the database before you 
change anything.


Regards, Hans-Rudolf

On 03/11/2014 11:58 PM, Ganote, Carrie L wrote:

Hi List,

I just pulled and merged from galaxy-dist (I think it's dc067a95261d),
updated my database, and migrated my tools. The issues I am able to see
are minor, but I have a user who can no longer access a particular
history. It apparently just hangs. If they delete the history, Galaxy
responds, but it will hang again when they try to add back any datasets.
Unfortunately, I don't see any errors in the paster logs about this. I
fear that their dataset entries in the Postgresql db have been corrupted
during the update, or perhaps the files themselves were purged. I cannot
reproduce their issues with my own histories - I'm able to bring up
saved histories and upload etc. I don't know if they can share a history
if it can't be loaded. How should I troubleshoot this?
I'm set up to authenticate through apache, which makes it harder to get
in as the user and see what's up. Is there an easy way to find out what
histories belong to what users? I can search the database?

Any advice would be greatly appreciated!

-Carrie


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Re: [galaxy-dev] error in workflow

[Hans-Rudolf Hotz]

Hi Milad

The error message: "database is locked" might be a hint.

Are you using a PostgreSQL database or just SQLite ? If the latter, you 
will often run in troubles when running more than one job at a time, due 
to file locking.


Regards, Hans-Rudolf


On 03/11/2014 07:41 PM, Milad Bastami wrote:

Dear Galaxy Developers,
I'm running galaxy local on ubuntu and trying to run a workflow on
multiple datasets (separately).  Occasionally when I try to run workflow
on input dataset I get "Unable to finish job" error in some steps, in
most time the problem will be solved when I run the workflow again, but
this going to happen more frequently. I attached the error message here.
I suspect it may be related to increase in number of datasets of the
current history (1757 datasets with ~350GB size).
I will appreciate your help

Traceback (most recent call last):
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py",
 line 116, in queue_job
 job_wrapper.finish( stdout, stderr, exit_code )
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py",
 line 1068, in finish
 self.sa_session.flush()
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
 line 114, in do
 return getattr(self.registry(), name)(*args, **kwargs)
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
 line 1718, in flush
 self._flush(objects)
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
 line 1804, in _flush
 transaction.commit()
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
 line 365, in commit
 t[1].commit()
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 2045, in commit
 self._do_commit()
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 2075, in _do_commit
 self.connection._commit_impl()
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 1280, in _commit_impl
 self._handle_dbapi_exception(e, None, None, None, None)
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 1277, in _commit_impl
 self.engine.dialect.do_commit(self.connection)
   File 
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
 line 307, in do_commit
 connection.commit()
OperationalError: (OperationalError) database is locked None None



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Re: [galaxy-dev] Galaxy database size and location

[Hans-Rudolf Hotz]

Hi Ravi

I don't quite understand question. It looks like you are mixing up two 
different things? A few comments, which might clarify and help you:


 - the postgresql db does not store the data. It tracks the users,
   their jobs and their histories. Hence, it stays pretty small.

 - the actual data is stored in ~/galaxy_dist/database/files/
   And this directory (or rather its numbered subdirectories) can grow
   pretty quickly - depending on the kind of jobs you run.

 - there are clean-up scripts which you can use to remove 'deleted'
   history items (ie the data), see: 
https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets



Hope this helps, Hans-Rudolf


On 03/06/2014 02:39 AM, Ravi Alla wrote:

Hi fellow galaxy devs,

I am trying to understand how to implement the galaxy database and get an idea 
of how big it could get. Currently we are running galaxy on a webserver, and 
want to have the postgresql db on locally mounted partition and not on an NFS 
partition. This limits us to around 100GB of storage for the db. We will create 
data libraries for users to load their data without copying to galaxy, so input 
files won't be duplicated. Is there anything we can do about the output files? 
Do these files need to end up in the database or can we put them on the NFS 
partition somewhere with the db holding information about their location?
I noticed that on a routine small analysis I could easily have 20GB or more of 
output files and history and all this is in the database.
If output files and history files are written to the database, are they cleaned 
up daily to avoid storage issues?

Please advise.
Thanks
Ravi Alla
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Re: [galaxy-dev] UCSC Display option

[Hans-Rudolf Hotz]

Hi Alper


Have a look at ~/galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt

check the line starting with

"main  http://genome.ucsc.edu/cgi-bin/hgTracks?";

and add mm10


do a restart and you should get the link to 'UCSC main' for data mapped 
to mm10



if that fixes the problem for UCSC, you can do the same for ensembl by 
fixing:


galaxy_dist/tool-data/shared/ensembl/ensembl_sites.txt



Regards, Hans-Rudolf






On 02/26/2014 08:01 PM, Alper Kucukural wrote:

Hi,

When I map the reads with bowtie2 to hg19.
I got the output like below and there are four display options. When I map the reads 
to mm10. I got only display in “IGB Local Web option". So, how can I fix this 
for mm10 or others and show all options?

101: Bowtie2 on data 4: aligned reads
91.6 KB
format: bam, database: hg18
[bam_header_read] EOF marker is absent. The input is probably truncated. 
[samopen] SAM header is present: 45 sequences. 2500 reads; of these: 2500 
(100.00%) were unpaired; of these: 1829 (73.16%) aligned 0 times 279 (11.16%) 
aligned exactly 1
display at UCSC main test
display at Ensembl May 2009
display with IGV web current local
display in IGB Local Web

Best,

Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: al...@kucukural.com




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Re: [galaxy-dev] Local Galaxy web layout

[Hans-Rudolf Hotz]

Hi Shenwiyn


Have a look at:

~/galaxy_dist/database/compiled_templates/base_panels.mako.py


Regards, Hans-Rudolf



On 02/17/2014 08:04 AM, shenw...@gmail.com wrote:

Galaxy developers:
I want to change my local  Galaxy web layout,for example,delete the top
button of "Visualization" and "Cloud" or change their positions.Could
anyone show me some details about this?
Thank you very much.


shenw...@gmail.com


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Re: [galaxy-dev] Galaxy Reports link - registed users per month - does not work

[Hans-Rudolf Hotz]

Hi Liisa

This rings a bell


I assume you use a MYSQL database? and I guess other pages are broken as 
well?


We are also using MySQL and I had to fix several lines in several files 
in order to get all report pages to work.


To do the fixes, have a look at this old (but still valid) e-mail from 
Assaf Gordon:


http://lists.bx.psu.edu/pipermail/galaxy-dev/2009-August/000641.html


I can send you all my fixed files next week


Regards, Hans-Rudolf







On 01/17/2014 05:38 PM, Liisa Koski wrote:

Hello,
First..I love the Galaxy Reports tool...thanks so much for this.

I did however come across an error when trying to few the Registered
Users per month link. It would be really nice to have this working :)

Thanks in advance,
Liisa


URL: http://domain:9001/users/registered_users_per_month

Module paste.exceptions.errormiddleware:*144* in __call___
__>> _
app_iter*=*
self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call___
__>> _
environ*,*
self*.*app*)*
Module paste.wsgilib:*543* in intercept_output_
__>> _
app_iter*=*
application*(*environ*,* replacement_start_response*)*
Module paste.lint:*170* in lint_app_
__>> _
iterator*=*
application*(*environ*,* start_response_wrapper*)*
Module paste.recursive:*84* in __call___
__>> _
*return*self*.*application*(*environ*,*
start_response*)*
Module paste.httpexceptions:*633* in __call___
__>> _
*return*self*.*application*(*environ*,*
start_response*)*
Module galaxy.web.framework.base:*132* in __call___
__>> _
*return*self*.*handle_request*(*
environ*,* start_response*)*
Module galaxy.web.framework.base:*190* in handle_request_
__>> _
body*=*
method*(* trans*,* kwargs*)*
Module galaxy.webapps.reports.controllers.users:*29* in
registered_users_per_month_
__>> _
*for*row*in*q*.*execute*():*
Module sqlalchemy.sql.expression:*2841* in execute
Module sqlalchemy.engine.base:*2453* in _execute_clauseelement
Module sqlalchemy.engine.base:*1584* in _execute_clauseelement
Module sqlalchemy.engine.base:*1698* in _execute_context
Module sqlalchemy.engine.base:*1691* in _execute_context
Module sqlalchemy.engine.default:*331* in do_execute
Module MySQLdb.cursors:*173* in execute
Module MySQLdb.connections:*36* in defaulterrorhandler*
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS
num_users \nFROM galaxy_user GROUP BY date_trunc(%s,
date(galaxy_user.create_time)) ORDER BY date DESC' ('month', 'month')*



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Re: [galaxy-dev] moving galaxy instance to different location

[Hans-Rudolf Hotz]

Hi Ido

Over the last few years, we have moved our production server to 
different hardware twice. And we also made copies of our production 
server in order to have the right development environment.


It always work without much hassle, once we have taken care of the 
'obvious', which usually was a combination of changing the absolute 
paths the configuration files and creating sym-links.



As always, make sure you have a back-up of your PostgreSQL (or MySQL) 
database.



Regards, Hans-Rudolf


On 01/16/2014 02:43 PM, Ido Tamir wrote:

Hi,

I have to move my galaxy instance to a different file system location.
Is there anything that I have to look out for besides the obvious like absolute 
paths in some data configs?

thank you very much,
ido



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[galaxy-dev] "allow_user_impersonation" (was: creating a hierarchy of students teachers and courses)

[Hans-Rudolf Hotz]

Hi

I am sorry for hijacking someone else's thread:




3.   teachers having read access to students’ work


This one is why I would give the teachers admin access - I think they
could impersonate the students to access their work (set
allow_user_impersonation = True in universe_wsgi.ini). It would mean
that every teacher would have full access to every students work - if
this is a problem you might want to consider standing up a Galaxy
instance per class - there is some up front overhead with this - but
it would make cleaning things up really easy.




"allow_user_impersonation" does not work when using external 
authentication. Are there any fixes for this in progress?


If not shall I create a Trello card?



Regards, Hans-Rudolf
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Re: [galaxy-dev] Avoid integrated_tool_panel.xml update

[Hans-Rudolf Hotz]

Hi Christian


Have a look at the file: .hgignore


Regards, Hans-Rudolf


On 01/16/2014 03:23 AM, Cristian Alejandro Rojas wrote:

Hi all,

There is a setting on somewhere to skip the integrated_tool_panel.xml
file update?

Best regards,

--
*Cristian Alejandro Rojas Quintero*
/*Estudiante Ingeniería de Sistemas */
/*Universidad Distrital Francisco José de Caldas*/
Bogotá - Colombia



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Re: [galaxy-dev] Quota problem

[Hans-Rudolf Hotz]

Hi Thomas


Just double checking: what value are you using for the 'days' option?

If you use the default (which is 60 days if I remember correctly), only 
data sets which have been 'deleted' more than 60 days ago will actually 
be removed.


Regards, Hans-Rudolf



On 01/14/2014 09:49 AM, Thomas Bellembois wrote:

Hello,

I am Thomas, IT engineer at the IGFL in France (http://igfl.ens-lyon.fr/).
We are running our own Galaxy instance in front of an OGE cluster.

Users quota never decrease when they delete items in their history. I
have run the scripts in the cleanup_datasets directory but without
success. I have no errors in the logs.

Any idea ?

Regards,

Thomas


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Re: [galaxy-dev] Careful data migration

[Hans-Rudolf Hotz]

Hi Sebastian

I am also not aware of any such documentation. It is probably impossible 
to write it, as each such situation is different.



I don't quite understand what your 'script' is doing, but in your 
situation, I recommend the following:


First of all, make sure you have a backup of your PostgreSQL (or MySQL) 
database.


Don't make any changes to 'universe.wsgi', but move the bulky 
directories to new locations on the NFS share and replace them with 
symbolic links. This has also the advantage, that you can do it step by 
step (ie directory by directory).



Regards, Hans-Rudolf

On 01/13/2014 05:33 PM, Sebastian Schaaf wrote:

Hi @ all,

I would like to know if anyone could give me some guidance or hint on
how to migrate data 'correctly' if Galaxy already wrote files, worked on
the database etc.

The situation is that we set up an instance, it was already in use and
wrote files e.g. into the directory 'galaxy-dist/database/'. The local
space is quite small, but more storage is available via a NFS share. I
already wrote a bash script for setting up the connections (and editing
the 'universe.wsgi' file accordingly) for the entries 'genome_data_path,
'ftp_upload_dir', 'file_path', 'new_file_path' and
'job_working_directory'. Those should address the most bulky features...
The application of that script is fine as long as the Galaxy system has
never started before. While applying that on a system that already 'did
something', e.g. the files in the 'database/' subdirectory remain there
and are not transferred. Anyhow, if Galaxy is started up after the
application of the new settings, no error is reported.

I wonder how Galaxy now deals with that situation:
* Handling data from both sources? (read and/or write?)
* Automatic movements of the 'historic' data when touched the next time?
* Crashes if those older objects are intended to be read/edited?
* Removes them silently from the database?

=> Is there a procedure/module to used in order to migrate the data? Is
it sufficient (and appropriate) just to move all contents of the old
folders to the new locations? Did I miss any existing documentation on
that issue?

The answer(s) may diverge, depending on to which of the five parameters
announced above those questions are addressed...

Any help appreciated before blowing up our production instance :).

Thanks in advance,
Best regards,
Sebastian






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Re: [galaxy-dev] galaxy local installation

[Hans-Rudolf Hotz]

Hi Edgar

please find my comments within your text below:

On 12/11/2013 06:30 PM, fernandez Edgar wrote:

Hello,

My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal.

I’ve been ask by a teacher to check out Galaxy.

So I’ve installed locally on my computer galaxy (I’m running openSUSE
x86_64 but I’ll install it on SUSE Linux ia64).

I’ve executed the run.sh script and I’ve somewhat successfully made the
website work.

I say somewhat because I have a couple of issues:

1.The website is not well displayed (refer to the attachment)


just double checking: have you reloaded your page?


2.I’ve changed the value of host to 0.0.0.0 in the universe_wsgi.ini
file and it still launches to 127.0.0.1


"127.0.0.1" seems correct to me, as this is the loopback address (ie 
'localhost'.




I was also wondering if there is a step by step tutorial to install all
the dependencies?

I’m finding myself overwhelmed with all the different dependencies.


well, I recommend, you first make a list of the tools you want to offer 
in Galaxy, and then figure out which dependencies you actually need. And 
then use these wiki pages:


https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies



Regards, Hans-Rudolf


Cordialement / Regards,

**

*Edgar Fernandez*

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

(  Bur. : *1-514-343-6111 poste 16568**//*

*//*

*/Université de Montréal/**//*

PAVILLON ROGER-GAUDRY, bureau X-218



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Re: [galaxy-dev] funny bug with latest galaxy release when using IE

[Hans-Rudolf Hotz]

Hi Ambrose


simple answer: don't use Explorer and use Firefox or chrome instead.

I have tested the Nov. 4th release before updating our production server 
and it worked on explorer 9 (on Windows 7). Nevertheless, I have been 
running into the same issue during our Galaxy training course this week. 
Again, the simple fix was to install Firefox



Hans-Rudolf





On 12/10/2013 06:28 PM, Ambrose Andongabo (RRes-Roth) wrote:

Dear All,

We get a very annoying behaviour using the latest release(04 November)
  of galaxy on Internet explorer. We tested it on I.E version 9 and
version 10 and we get the same behaviour as you can see from the
screenshot below

I hope there is somebody who knows why this is happening

Thanks

Ambrose


--
This message has been scanned for viruses and
dangerous content by *MailScanner* , and
we believe but do not warrant that this e-mail and any attachments
thereto do not contain any viruses. However, you are fully responsible
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Re: [galaxy-dev] survey

[Hans-Rudolf Hotz]

On 12/02/2013 11:14 PM, Philippe Moncuquet wrote:

Hi,

I hope this is relevant to the dev list but if it is not please let me know.

I was trying to estimate active users out of our registered users. I
ended counting users that had a job during the last month. How would you
guys do ?


I assume, you are also using the 'report tools'?

In general it is difficult to do the estimate, ie what is the difference 
between a user who does 5 jobs every month and a user who does 50 jobs 
at once and then never uses Galaxy again?


Hence, I would count the total number of jobs. Although, again, the 
number could be misleading, as there are 'big' jobs and 'small' jobs 
which use different amounts of compute resources, and so on




During this process I also wanted to see how we were doing in comparison
to other instance. I set up a simple survey and would greatly appreciate
if instance admin would take 2 min to complete it. I will publish
results here (or maybe to some more relevant place, let me know) at the
end of the month.

https://fr.surveymonkey.com/s/CD6NN88



done.


Regards, Hans-Rudolf



Regards,
Philip


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Re: [galaxy-dev] Lock Galaxy job submission

[Hans-Rudolf Hotz]

Hi Peter

No, you are not imagining things. It has been removed. I guess, this was 
the commit:


https://bitbucket.org/galaxy/galaxy-central/commits/445b212b1c6d/


Though, we used this features very often in the early days, I didn't 
notice it was gone (maybe because, I have turned harsh and just kill 
jobs when people don't listen to announcements about scheduled a system 
shutdown).


Nevertheless, I have added a Trello card
https://trello.com/c/BTDaHy9m/1269-re-institute-job-lock-feature

Hans-Rudolf



On 11/20/2013 03:31 PM, Peter Cock wrote:

Hello all,

It is my recollection that under the "Admin" panel, "Manage jobs"
page, there used to be a toggle control to lock the submission
of new jobs. This was very helpful in preparation for scheduling
a system shutdown (e.g. for hardware or software updates).

However, I no longer see this option on either galaxy-central
or galaxy-dist. Was it removed, or am I imagining things - in
which case should I file an enhancement request ;)

(I've had a look in Trello and didn't find anything)

Thanks,

Peter
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Re: [galaxy-dev] Trouble setting up a local instance of Galaxy

[Hans-Rudolf Hotz]

Hi Starr


I will try to answer some of your questions. Next time I recommend to 
ask just one question (with a corresponding subject line). This will 
make it much easier for the community to help you, and for others with 
similar problems to find the correct e-mail thread.


see below for my answers...

On 11/06/2013 11:43 PM, Hazard, E. Starr wrote:

Hello,
I am a new user of Galaxy.
I have a Galaxy instance running (sort of)  on a local research cluster.
I issued the command "hg update stable” today and it retrieved no files.
SO presume I am up-to-date on the stable release. I start the instance
as a user named “galaxy”.
Right now I am still running in “local” mode. I hope to migrate to DRMAA
LSF eventually.
I have tried to set up ProFTP to upload files but have not succeeded so
I use Galaxy Web-upload.
The upload was working nicely and I had  added  a couple of  new tools
and they were working with the uploaded files.
Getting LSF/DRMAA to work was giving me fits and ultimately I deleted
all my history files in an effort to start over.
Presently, files being uploaded appear in history as say job 1 ( in a
new history) The job status in the history panel of the web GUI
changes from purple to yellow then then to red indicating some sort of
error. There is no viewable error text captured, but I can click on the
“eye” icon and see the
first megabyte of the data (for tiny files I can see the entire content
and it’s intact). In the Galaxy file system, however, these files appear
but have a different number , say, dataset_399.dat

On my system the uploaded files appear in
/PATH/galaxy-dist/database/files/000

My first question is why is the data going into the “000” subdirectory
and not one “owned’ by the user who is uploading?


all files are owned by galaxy (independent of who is uploading them 
and/or generate new files). The first 1000 files are stored in '000', 
the next 1000 files in '001', and so on.


Access permission is handled by the SQLite database (unless you have 
already switched to a  PostgreSQL database).




My second question is why is the dataset being labeled as
dataset_399.dat and not dataset_001.dat?


The number is given by the SQLite database. When you want a clean start, 
you need to remove all files from ~/database/files/000 and start with an 
empty database.



My third question is why do the uploaded files not appear as selectable
options ( say I have paired-end fastq files and tool wants to have
choices about filenames)? This problem is present for programs that seek
one input file as well.


When you uploaded the files, was the 'format' properly recognized?



  I presume that Galaxy is confused because the numbering in history is
not the same as the numbering in the file upload archive (e.g.
/PATH/galaxy-dist/database/files/000 in my case) so my last question is
how do I “reset” my system to get the dataset and history numbers to be
the same?


The numbering in the history has nothing to do with the file numbering. 
See above wrt my comment about a 'clean start'



Regards, Hans-Rudolf



Here’s how I launch the Galaxy instance

  sh /shared/app/Galaxy/galaxy-dist/run.sh -v --daemon
--pid-file=Nov6Localdaemon.pid.txt  --log-file=Nov6Local1639daemon.log.txt

Entering daemon mode


Here are the last lines of the log

Starting server in PID 26236.

serving on 0.0.0.0:8089 view at http://127.0.0.1:8089


galaxy.tools.actions.upload_common DEBUG 2013-11-06 16:48:49,624
Changing ownership of
/shared/app/Galaxy/galaxy-dist/database/tmp/upload_file_data_QZGHm4
with: /usr/bin/sudo -E scripts/external_chown_script.py
/shared/app/Galaxy/galaxy-dist/database/tmp/upload_file_data_QZGHm4
hazards 502

galaxy.tools.actions.upload_common WARNING 2013-11-06 16:48:49,750
Changing ownership of uploaded file
/shared/app/Galaxy/galaxy-dist/database/tmp/upload_file_data_QZGHm4
failed: sudo: no tty present and no askpass program specified


galaxy.tools.actions.upload_common DEBUG 2013-11-06 16:48:49,751
Changing ownership of
/shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO with:
/usr/bin/sudo -E scripts/external_chown_script.py
/shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO hazards 502

galaxy.tools.actions.upload_common WARNING 2013-11-06 16:48:49,775
Changing ownership of uploaded file
/shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO failed: sudo: no
tty present and no askpass program specified


galaxy.tools.actions.upload_common INFO 2013-11-06 16:48:49,805 tool
upload1 created job id 170


galaxy.jobs DEBUG 2013-11-06 16:48:50,678 (170) Persisting job
destination (destination id: local)

galaxy.jobs.handler INFO 2013-11-06 16:48:50,698 (170) Job dispatched

galaxy.jobs.runners.local DEBUG 2013-11-06 16:48:50,994 (170) executing:
python /shared/app/Galaxy/galaxy-dist/tools/data_source/upload.py
/depot/shared/app/Galaxy/galaxy-dist
/shared/app/Galaxy/galaxy-dist/database/tmp/tmpTq22ot
/shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO
406:/shared/app/Galaxy/galaxy-dist/database

Re: [galaxy-dev] browse directories on galaxy server

[Hans-Rudolf Hotz]

Hi David


Using "Data Libraries", as suggested by Martin is definitely the way to 
go. Especially if you want to use the files with different tools.


However, if you have a predefined set of tools, you might wanna consider 
adding an extra tools which reads and process the files, eg: you have 
your raw fastq files in a central location and you always do the same 
pre-processing steps. For such a case, I recommend using the 
"dynamic_options" attribute. This allows you to present a list of files, 
which you can then select from and do the processing on.


May I refer to a similar question for the details on how to implement this:

http://tinyurl.com/6uom4uo
(I can give you more details if interested)


Of course, you can go to the extreme case, and just trigger a copy of 
the selected file into your history. But this will end up in data 
duplication and you wanna avoid this.


Regards, Hans-Rudolf




On 11/01/2013 01:46 AM, Martin Čech wrote:

Hello David,

please see whether Data Libraries
(http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries) with the
file import
(http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles) and
especially the /Upload files from filesystem paths/ feature do solve
your problem. It enables you to work with the datasets while keeping
them untouched on the file system.

thank you for using Galaxy!

regards

Martin

On Thu, Oct 31, 2013 at 3:05 PM, David Hoover mailto:hoove...@helix.nih.gov>> wrote:

Is there any desire to create a way in galaxy to browse local
directories on the galaxy server itself?  Not the client machine
running the web browwser, but the machine on which galaxy is
running.  I've created a tool that allows a user to upload a single
file from their own personal directory on the galaxy server into
galaxy directly, without going through Apache.  However, this is
very limiting.  It would be very helpful to be able to browse
directories that are deemed accessible to the galaxy user, and
before I begin trying to develop anything I'd like to know if there
is any support for such a feature.

David Hoover
Helix Systems Staff
National Institutes of Health
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Re: [galaxy-dev] [galaxy-user] Inquiring

[Hans-Rudolf Hotz]

Hi Yan

Assuming you have copied everything to the new server and you have 
changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' 
file it should all work


Regards, Hans-Rudolf


On 10/31/2013 04:36 PM, Yan Luo wrote:

Dear All,

We have a question regarding the Galaxy server. We installed a local
version on our Linux machine and need move to a new place. The IP
address will be changed. Could you please let me know if the server can
be still used? I mean, we can use the new IP to open the home page of
Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which
is similar as before(I just replace the IP address). Do we need reset
anything for Galaxy? Will the Galaxy use the fixed IP address in the
system when it was installed?

xxx.xxx.xxx.xxx:8080/root

Looking forward to hearing from you.

Best Wishes,

Yan


On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor mailto:n...@bx.psu.edu>> wrote:

Hi Yan,

I've moved this discussion to the galaxy-dev list since it pertains to a
local installation of Galaxy.

Responses to your questions follow, in-line.

Yan Luo wrote:
 > Dear Sir,
 >
 > (1)We installed Galaxy, but recently the user can't registered
and got the
 > following error, how can we fix it?
 >
 > Sever error
 > An error occurred. See the error logs for more information.(To
turn debug on
 > to display ...).

Since debug = False in universe_wsgi.ini, you should be able to find a
more detailed error message in the log file.  If starting Galaxy with:

   % sh run.sh --daemon

The default log file is 'paster.log' in Galaxy's root directory.

 > (2) Could you please let me know if there is any command to stop
galaxy?

If starting with the --daemon flag (as above), you can use:

   % sh run.sh --stop-daemon

If running in the foreground, you can use Ctrl-C to terminate the
process.  There is a recent bug whereby Ctrl-C is ineffective on some
platforms under Python 2.6 - in this case you will have to kill/pkill
the process manually.  We are working on a fix for the latter.

 > (3) If I reset universe_wsgi.ini file and want to set an
administrator
 > user(I can add a line in the above file), how can I get the
password? Should
 > I stop galaxy(See question 2) first? then run "./setup.sh" and
"./run.sh".

setup.sh would have only been necessary prior to running Galaxy the
first time, however, this step has recently been removed.  If you are
referencing documentation that still refers to setup.sh, please let us
know so we can update it - I did notice this was still on the
"Production Server" page, so I removed it from there.

You no longer need to run setup.sh at all.

 > (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be
generated?
 > if I want to change this file,should I edit it before "run.sh"
and after
 > "setup.sh". Is it right?

setup.sh and its replacements in run.sh and the Galaxy application
itself never overwrite files, they only create files from sample files
if they do not exist.

 > (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and
 > "./setup.sh"(./run.sh), which one is correct under Linux?

Both syntaxes are effectively the same in most cases.

--nate

 >
 > Looking forward to hearing from you.
 >
 > Best Wises,
 >
 > Yan Luo, Ph.D.
 > NIH
 >


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 > galaxy-u...@lists.bx.psu.edu 
 > http://lists.bx.psu.edu/listinfo/galaxy-user




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Re: [galaxy-dev] How we found the filenames of all of the Galaxy datasets

[Hans-Rudolf Hotz]

Hi Yaron

This is useful - Thank you very much.

Coming up with such a sql statement to identify the files from people 
who have left our institute has been on my list of things to do for 
quite some time.


Now I just need to figure how to distinguish the files which have been 
shared with people who are still here.



Regards, Hans-Rudolf

PS: for those of us who got stuck with a MySQL database, this is the 
corresponding select statement:


SELECT CONCAT(substring(lpad(history_dataset_association.dataset_id, 6, 
00) from 1 for 3), '/dataset_', 
history_dataset_association.dataset_id, '.dat') AS file, 



On 10/30/2013 10:00 AM, Yaron de Leeuw wrote:

Hi.

During IT housekeeping, we have decided that we must know the filenames
of all of the galaxy datasets in our local deployment. Searching the docs
and
the web yielded no reasonable answer, so we figured we'll just write our
own tool.
At first, we thought about a Galaxy tool, but found no way to extract all
the
datasets of all histories. So we went deeper. To the SQL itself.

Without further ado, I give you the query:

 SELECT substring(to_char(history_dataset_association.dataset_id,
'00') from 2 for 3) ||  '/dataset_' ||
history_dataset_association.dataset_id || '.dat' ,
history_dataset_association.create_time, history_dataset_association.name,
history_dataset_association.extension, history.name AS
history_name,galaxy_user.username
 FROM history_dataset_association
 JOIN history ON history_dataset_association.history_id = history.id
 JOIN galaxy_user ON history.user_id = galaxy_user.id
 WHERE history_dataset_association.deleted = false AND
history_dataset_association.purged = false
 ORDER BY  username, history_name, create_time;

We use PostgreSQL, so to run this you save the query as
`get_filenames.sql`, and run:

 psql -U galaxy galaxy_prod -f get_filenames.sql -A >
galaxy_export_filenames.csv

This prints out a line structured as:
003/dataset_3748.dat|2012-10-09 12:07:37.786751| index.fastq|fastq|nan|sean

Which means:
   folder/filename  |  time of creation  |  name as appears in history  |
format  |  history name |  history owner

Only files that were not deleted in galaxy are printed (you can remove the
"WHERE"
line if you want them all).

By the way, one of the main struggles was finding the folder/filename. We
have searched
the database repeatedly for a filename field to no avail, until someone
recognised
the fact that they can be derived from the dataset_id. If you zero pad the
id to six chars,
the first three chars would be your folder name. The whole id is the file
name. e.g.:
dataset_id = 12345
folder = 012
filename = dataset_12345.dat


Yaron.

Search engine candies:   export migrate files datasets filenames on disk



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Re: [galaxy-dev] about the sqlalchemy-migrate

[Hans-Rudolf Hotz]

Hi "ngsf...@hygenomics.com"

You ask four different questions. I strongly recommend you ask them in 
four different mails each with an appropriate subject line, next time.

This will make it much easier for the community to help you.
Also, copy paste the logs and don't use screenshots, as they will get 
lost in the reply.


On 10/14/2013 10:08 AM, ngsf...@hygenomics.com wrote:> hi,all:
> 1. when I started the galaxy daemon. In the paster.log has a
> warning.who can help me. url= 
http://code.google.com/p/sqlalchemy-migrate/


When you start galaxy a second time, do you still get the error?
Can you manually fetch the egg?

>  2. missing file.

It is just a warning: You don't provide the index files. Do you really 
need all those tools?


This page will probably help you:

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

>  3.What should I do about it?

You don't provide an "job_conf.xml" file. It still works, as explained 
in the warning message. Altenatively, have a look at


~/galaxy_dist/job_conf.xml.sample_advanced
~/galaxy_dist/job_conf.xml.sample_basic


>  4.What should I do about it?

Again, just warnings. You need to investigate the individual tool xml files


Hope this helps

Regards, Hans-Rudolf



> 
> ngsf...@hygenomics.com
>
>
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> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Tabular data not displaying in main panel

[Hans-Rudolf Hotz]

Hi Peter and Bjoern

we had similar problems in August, when we upgraded to 
'release_2013.06.03'. The problem has disappeared now.


At the time I had the suspicion, it only happened to browser sessions 
which were already open before the upgrade, Hence, closing the browser, 
and starting again helped. But this was just a guess.



Regards, Hans-Rudolf


On 10/02/2013 08:48 PM, Björn Grüning wrote:

Hi Peter,

we can confirm. Latest Galaxy stable version and its occurring randomly.
I was not able to reproduce it by myself.

Cheers,
Bjoern


Hi all,

Multiple users of our internal Galaxy server have reported with
multiple browsers that tabular data is not displayed in the main
central panel. The preview in the history works, but clicking on
the "eye" icon gives a blank page.

I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML
for the central frame looks blank but is actually a script when
viewed via the frame source. The tabular file data is there in
the script's first_data_chunk entry - but does not get shown.
An except is shown below.

Has anyone else noticed this problem? I believe it began
when I last updated this Galaxy instance, but was not
noticed immediately.

Thanks,

Peter

---

I believe we are running the current stable release, or at least
the latest commit on the default branch from galaxy-dist

$ hg pull
warning: bitbucket.org certificate with fingerprint
24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not
verified (check hostfingerprints or web.cacerts config setting)
real URL is https://bitbucket.org/galaxy/galaxy-dist
pulling from http://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found

$ hg update
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ hg branch
default

[galaxy@ppserver galaxy-dist]$ hg log -b default | head
changeset:   10411:c42567f43aa7
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.

changeset:   10410:e9ee9c5d30ae
user:Dave Bouvier 
date:Mon Aug 19 13:08:45 2013 -0400
summary: Remove duplicate method from the install and test's
functional_tests.py.
...


---



 
 
 Dataset Display
 

 

 









 

 

 
 // console protection
 window.console = window.console || {
 log : function(){},
 debug   : function(){},
 info: function(){},
 warn: function(){},
 error   : function(){},
 assert  : function(){}
 };

 // Set up needed paths.
 var galaxy_paths = new GalaxyPaths({
 root_path: '/galaxy/',
 image_path: '/galaxy/static/images'
 });
 



 
 

 
 require.config({
 baseUrl: "/galaxy/static/scripts",
 shim: {
 "libs/backbone/backbone": { exports: "Backbone" },
 "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
 }
 });

 require(['mvc/data'], function(data) {
 data.createTabularDatasetChunkedView(
 _.extend( {"misc_blurb": "7,891 lines", "peek":
"
1
2
3
Gpa_EST_02_04___C05_022
GO:0005737
...
",
"data_type": "tabular", "deleted": false, "history_id":
"cdbf837ba6516a14", "metadata_column_names": null, "visible": true,
"genome_build": "?", "hid": 10, "file_size": 509095,
"metadata_data_lines": 7891, "file_ext": "tabular", "id":
"0ddcd2cf2375e24a", "misc_info": "\nBLASTX output identified\nInput
has 4507 queries\nDone\nStandard out:\nBlast2GO Pipeline Version
2.5.0\n--\n\nHash for resource
ec2go_19072011.txt of type ec created. 4003 associations
loaded.\nBlast2GO build: 23092011\nChange ", "hda_ldda": "hda",
"name": "Blast2GO Local database (May 2011)", "metadata_columns": 3,
"uuid": null, "state": "ok", "metadata_comment_lines": null,
"model_class": "HistoryDatasetAssociation", "metadata_dbkey": "?",
"purged": false, "metadata_column_types": ["str", "str", "str"]},
 {
 url_viz: "/galaxy/visualization",
 chunk_url:
"/galaxy/dataset/display?dataset_id=0ddcd2cf2375e24a",
 first_data_chunk: {"ck_index": 1,
"ck_data": "Gpa_EST_02_04___C05_022\tGO:0005737\tn-dimethylarginine
dimethylaminohydrolase\n...\n"}
 }
 ),
 // Append view to body.
 $('body')
 );
 });
 

 
 

 


--
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Please keep all replies on the list by using "

Re: [galaxy-dev] Dynamic data library

[Hans-Rudolf Hotz]

On 10/01/2013 07:12 PM, Cole, Nathan (NIH/NCI) [C] wrote:

One final question as I dive into looking at these two methods:  can you expose whole 
hierarchies and directories using the "from_file" method or will this only work 
on an individual sample basis?


yes, you can.
as an example have a look at the affymetrix cel files we offer. See 
attachment for a screen shot and the coresponding fragment from the xml 
file:


  
  
value="HumanGeneST10_TissueData">
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_01_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_02_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_03_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_01_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_02_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_03_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_01_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_02_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_03_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_01_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_02_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_03_mGENE.CEL"/>

//
  value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Thymus_03_mGENE.CEL"/>


value="MouseGeneST10_TissueData">
  value="/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Brain_01_mGENE.CEL"/>
  value="/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Brain_02_mGENE.CEL"/>

//
  value="/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Thymus_03_mGENE.CEL"/>


  
  
//
  






If not, is there any method for exposing a the whole of a directory on the file 
system?

Thanks,
Nathan


-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Tuesday, October 01, 2013 10:11 AM
To: Cole, Nathan (NIH/NCI) [C]
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] Dynamic data library



On 10/01/2013 03:53 PM, Cole, Nathan (NIH/NCI) [C] wrote:

Thank you both for your responses.  I will be looking into both of these.

With regard to the from_file option to add the sample selection into the tool:  
I assume this means that the metadata and everything is loaded into galaxy at 
the time the tool is run.


This depends on how you write your tool. Do you just wanna read the ie fastq 
file or do you also wanna read the meta data. Also, how is the meta data 
accessible? eg. is it stored in a txt file at the same location as the fastq 
file?

  > Does this create a copy of the loaded file or simply read it in place?  
Also are there any efficiency issues created using this method, outside of the 
tool run time increase due to the load of the data taking place in-tool?

It should just read it in place

Hans-Rudolf



Thanks,
Nathan

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Tuesday, October 01, 2013 4:07 AM
To: Cole, Nathan (NIH/NCI) [C]
Cc: Martin Čech; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Dynamic data library

Hi Nathan


Do you have many tools working with those samples or just a few? If you only 
have a limited, predefined set of tools you might wanna consider adding the 
sample selection into the tool.

You can use the from_file, or from_data_table options to dynamically
create sample selection list. You can even drill down a hierarchical
list. Have a look at
~/tools/annotation_profiler/annotation_profiler.xml
which uses the file
~/tool-data/annotation_profiler_options.xml

All you need to do is keeping the file in sync with the directory
structure of your samples directory


Regards, Hans-Rudolf






On 09/30/2013 09:48 PM, Martin Čech wrote:

Hi Nathan,

Dannon answered similar question few days ago:

  There's an import mechanism in libraries that'll allow you to simply
  link to the file on disk without copy/upload.  I believe the
  "example_watch_folder.py" sample script (in the distribution) does
  just this via the API, if you want an example.


This might be what you are looking for.

Martin


On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C]

Re: [galaxy-dev] Dynamic data library

[Hans-Rudolf Hotz]

On 10/01/2013 03:53 PM, Cole, Nathan (NIH/NCI) [C] wrote:

Thank you both for your responses.  I will be looking into both of these.

With regard to the from_file option to add the sample selection into the tool:  
I assume this means that the metadata and everything is loaded into galaxy at 
the time the tool is run.


This depends on how you write your tool. Do you just wanna read the ie 
fastq file or do you also wanna read the meta data. Also, how is the 
meta data accessible? eg. is it stored in a txt file at the same 
location as the fastq file?


> Does this create a copy of the loaded file or simply read it in 
place?  Also are there any efficiency issues created using this method, 
outside of the tool run time increase due to the load of the data taking 
place in-tool?


It should just read it in place

Hans-Rudolf



Thanks,
Nathan

-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Tuesday, October 01, 2013 4:07 AM
To: Cole, Nathan (NIH/NCI) [C]
Cc: Martin Čech; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Dynamic data library

Hi Nathan


Do you have many tools working with those samples or just a few? If you only 
have a limited, predefined set of tools you might wanna consider adding the 
sample selection into the tool.

You can use the from_file, or from_data_table options to dynamically create 
sample selection list. You can even drill down a hierarchical list. Have a look 
at ~/tools/annotation_profiler/annotation_profiler.xml
which uses the file
~/tool-data/annotation_profiler_options.xml

All you need to do is keeping the file in sync with the directory structure of 
your samples directory


Regards, Hans-Rudolf






On 09/30/2013 09:48 PM, Martin Čech wrote:

Hi Nathan,

Dannon answered similar question few days ago:

 There's an import mechanism in libraries that'll allow you to simply
 link to the file on disk without copy/upload.  I believe the
 "example_watch_folder.py" sample script (in the distribution) does
 just this via the API, if you want an example.


This might be what you are looking for.

Martin


On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C]
mailto:nathan.c...@nih.gov>> wrote:

 Hello, we’ve set up a local Galaxy instance in our genotyping and
 next-gen sequencing lab with local Apache LDAP (AD) integration, NFS
 mounts to a large NAS, and cluster integration coming.  Do to the
 high volume of samples and staff that will be using the system, I
 want to set up data libraries (without copying to Galaxy).  This is
 obviously no problem the first time, however I was wondering if
 there was a way to make a library, added from a system path, be
 dynamic so that it would stay synchronized with the underlying file
 structure?

 __ __

 If a try dynamic library is not possible, is there a method for
 adding files to an existing library via that same system path that
 would not duplicate all of the original files in the data library?

 __ __

 I did some scouring of the list and found some old unanswered
 questions and some things tangentially related topics, but I was
 unable to find a true answer or solution to my problem.  Any
 information on how to do the tasks above or other solutions to
 provide the same functionality would be greatly appreciated.

 __ __

 Thanks,

 Nathan

 __ __


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Re: [galaxy-dev] Dynamic data library

[Hans-Rudolf Hotz]

Hi Nathan


Do you have many tools working with those samples or just a few? If you 
only have a limited, predefined set of tools you might wanna consider 
adding the sample selection into the tool.


You can use the from_file, or from_data_table options to dynamically 
create sample selection list. You can even drill down a hierarchical 
list. Have a look at

~/tools/annotation_profiler/annotation_profiler.xml
which uses the file
~/tool-data/annotation_profiler_options.xml

All you need to do is keeping the file in sync with the directory 
structure of your samples directory



Regards, Hans-Rudolf






On 09/30/2013 09:48 PM, Martin Čech wrote:

Hi Nathan,

Dannon answered similar question few days ago:

There's an import mechanism in libraries that'll allow you to simply
link to the file on disk without copy/upload.  I believe the
"example_watch_folder.py" sample script (in the distribution) does
just this via the API, if you want an example.


This might be what you are looking for.

Martin


On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C]
mailto:nathan.c...@nih.gov>> wrote:

Hello, we’ve set up a local Galaxy instance in our genotyping and
next-gen sequencing lab with local Apache LDAP (AD) integration, NFS
mounts to a large NAS, and cluster integration coming.  Do to the
high volume of samples and staff that will be using the system, I
want to set up data libraries (without copying to Galaxy).  This is
obviously no problem the first time, however I was wondering if
there was a way to make a library, added from a system path, be
dynamic so that it would stay synchronized with the underlying file
structure?

__ __

If a try dynamic library is not possible, is there a method for
adding files to an existing library via that same system path that
would not duplicate all of the original files in the data library?

__ __

I did some scouring of the list and found some old unanswered
questions and some things tangentially related topics, but I was
unable to find a true answer or solution to my problem.  Any
information on how to do the tasks above or other solutions to
provide the same functionality would be greatly appreciated.

__ __

Thanks,

Nathan

__ __


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Re: [galaxy-dev] Problem with get data/uploading file.

[Hans-Rudolf Hotz]

Hi Luobin

we had a similar situation with one of our development Galaxy 
installations, when our sysadmin changed (without telling us) the proxy 
settings of the server.



Regards, Hans-Rudolf

On 09/30/2013 07:35 PM, Luobin Yang wrote:

Hi, guys,

Recently I found the Upload File tool under the Get Data category runs
forever on my locally installed Galaxy system. It worked fine for a long
time, but now it's not working anymore. Have you guys experienced
similar things?

Thanks,
Luobin


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Re: [galaxy-dev] Limit number of Jobs to Trinity

[Hans-Rudolf Hotz]

well, I was just reading today's commits and I spotted: Nate's commit: 
"Bugfix for tool-to-destination mapping, tool ids are lowercased but the 
mapping id was not lowercased." - Changeset:   0b955e54451c


So I changed:

   

to

  


and it seems to work.

Regards, Hans-Rudolf


On 09/26/2013 05:43 PM, Hans-Rudolf Hotz wrote:

Hi Carlos and John

Please allow me to pick up this thread.

I have been experimenting with this, but I cant get it to work. The
default destination is always used. Does it work for you, Carlos?

Regards, Hans-Rudolf

On 09/23/2013 03:32 AM, John Chilton wrote:

As your Galaxy instance becomes more production ready I would
definitely recommend installing a job queue such as grid engine,
Torque, or SLURM. For this simple use case though, you should be able
t define multiple local job runner instances to ensure only one
Trinity job runs a time.

Your job_conf.xml should look something like this:



 
 
 
 
 
 
 
 
   
   
 
 
   
 


Hope this helps.

-John

On Sat, Sep 21, 2013 at 10:40 AM, Carlos Canchaya
 wrote:

Hi adam,

So far we have just a standalone server since we are still setting up
our
tools (we will scale up to our sge cluster, though). Any clue how to
limit
jobs per tool basis?

Best,

Carlos

On Saturday, September 21, 2013, Adam Brenner wrote:


Carlos,

Are you using any sort of scheduler? SGE/Torque, etc? How are jobs
being
dispatched to your node(s)? More info here:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster


--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya 
wrote:


Hi guys,

I have a running local galaxy installation on one of our servers.
I've
just installed Trinity for de novo assembly of transcripts and it
will use
up to 32 processors. However i would like to limit the number of
concurrent
jobs only for this tool. Do you know if it would be possible to
limit the
number of concurrent jobs per tool basis?

Bests,

Carlos

--
Carlos  Canchaya


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--
Carlos A. Canchaya
Universidade de Vigo


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Re: [galaxy-dev] Limit number of Jobs to Trinity

[Hans-Rudolf Hotz]

Hi Carlos and John

Please allow me to pick up this thread.

I have been experimenting with this, but I cant get it to work. The 
default destination is always used. Does it work for you, Carlos?


Regards, Hans-Rudolf

On 09/23/2013 03:32 AM, John Chilton wrote:

As your Galaxy instance becomes more production ready I would
definitely recommend installing a job queue such as grid engine,
Torque, or SLURM. For this simple use case though, you should be able
t define multiple local job runner instances to ensure only one
Trinity job runs a time.

Your job_conf.xml should look something like this:



 
 
 
 
 
 
 
 
   
   
 
 
   
 


Hope this helps.

-John

On Sat, Sep 21, 2013 at 10:40 AM, Carlos Canchaya  wrote:

Hi adam,

So far we have just a standalone server since we are still setting up our
tools (we will scale up to our sge cluster, though). Any clue how to limit
jobs per tool basis?

Best,

Carlos

On Saturday, September 21, 2013, Adam Brenner wrote:


Carlos,

Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being
dispatched to your node(s)? More info here:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster


--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya 
wrote:


Hi guys,

I have a running local galaxy installation on one of our servers.  I've
just installed Trinity for de novo assembly of transcripts and it will use
up to 32 processors. However i would like to limit the number of concurrent
jobs only for this tool. Do you know if it would be possible to limit the
number of concurrent jobs per tool basis?

Bests,

Carlos

--
Carlos  Canchaya


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--
Carlos A. Canchaya
Universidade de Vigo


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Re: [galaxy-dev] Creating Galaxy Admin / Local Install Mailing List - Updates?

[Hans-Rudolf Hotz]

Hi Adam

I guess the latest is written down in the notes for the GalaxyAdmins BoF 
at GCC2013, see:


http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins


maybe we can discuss this again at the next 'meetup'?

The next 'meetup' is scheduled for September 18, but I don't know 
whether it will happen? I am sure Dave will know more.



Regards, Hans-Rudolf





On 09/12/2013 04:52 AM, Adam Brenner wrote:

Howdy,

I know this has been discussed before, but I can not find the email
threads on this...but what was the status on creating a galaxy admin /
local install mailing list?

The Devel list is very chatty and while my filters do a good job, I
think it will be easier for others to find help on their own if it was
on a separate mailing list It would be easier to search and look
back at previous threads.

However, the added benefit of having the devel list is that we get
feedback from Galaxy Developers

As the saying godes: Just food for thought,
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
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Re: [galaxy-dev] Stable Galaxy for local install

[Hans-Rudolf Hotz]

Hi cngbgalaxy

May be there is an issue with the version of grep you are using on the 
server Galaxy is running on? I vaguely remember discussions on the 
mailing list related to grep/sort/etc


what happens when do it on the command line, ie:

[hrh@foo]$ grep "^@" foo.sam
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:10001
@SQ SN:chr2 LN:11
@SQ SN:chr3 LN:10001
@SQ SN:chr4 LN:1001
@RG ID:rg1 SM:s1
@RG ID:rg2 SM:s3
[hrh@foo]$ grep -v "^@" foo.sam
bar:record:477  chr11   0   *   *   0   0   
A   1   RG:Z:rg1
bar:record:677  chr11   0   *   *   0   0   
A   1   RG:Z:rg2
[haruhotz@xenon1 20130912]$



Alternatively, if everything fails, and all you wanna do is just 
removing the seven lines at the top of the sam file, you can also use 
the tool: "Text Manipulation" -> "Remove beginning of a file"




Regards, Hans-Rudolf


On 09/12/2013 06:07 AM, cngbgal...@gmail.com wrote:

Hi Adam Brenner,
This is my running steps.

  * I got my sam file (as follow) upload:

@HD VN:1.0 SO:coordinate

@SQ SN:chr1 LN:10001

@SQ SN:chr2 LN:11

@SQ SN:chr3 LN:10001

@SQ SN:chr4 LN:1001

@RG ID:rg1 SM:s1

@RG ID:rg2 SM:s3

bar:record:4



77



chr1



1



0



*



*



0



0



A



1



RG:Z:rg1

bar:record:6



77



chr1



1



0



*



*



0



0



A



1



RG:Z:rg2

bar:record:1



77



chr1



10



0



*



*



0



0



A



1



RG:Z:rg1

bar:record:3



77



chr1



10



0



*



*



0



0



A



1



RG:Z:rg2

bar:record:5



141



chr3



40



0



*



*



0



0



C



2



RG:Z:rg1

bar:record:9



77



chr4



10



0



*



*



0



0



A



1



RG:Z:rg1

bar:record:7



141



chr4



20



0



*



*



0



0



C



2



RG:Z:rg1

bar:record:5



77



chr1



40



0



*



*



0



0



A



1



RG:Z:rg2

bar:record:6



141



chr1



50



0



*



*



0



0



C



2



RG:Z:rg2

bar:record:2



77



chr2



10



0



*



*



0



0



A



1



RG:Z:rg1

bar:record:2



141



chr2



30



0



*



*



0



0



C



2



RG:Z:rg2

bar:record:3



141



chr3



20



0



*



*



0



0



C



2



RG:Z:rg1

bar:record:9



141



chr4



60



0



*



*



0



0



C

  

Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

[Hans-Rudolf Hotz]

Hi Thon

double check your datatypes_conf.xml (which was not touched/changed 
during the update process, since it is listed in the .hgignore file, I 
guess) with the new datatypes_conf.xml.sample file for any changes 
regarding converters for "bed" files



Regards, Hans-Rudolf


On 08/22/2013 02:51 AM, Anthonius deBoer wrote:

Yep...

$ bedtools --version
bedtools v2.17.0

Thon

On Aug 21, 2013, at 01:40 PM, sam guerler  wrote:


Hi Anthonius,

Do you have the BEDTools installed and its directory added to your
PATH environment variable? Trackster uses compressed file formats to
reduce the amount of data transfers.

I hope this helps,
Sam




On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer mailto:thondeb...@me.com>> wrote:

Hi,

I am using the latest version of galaxy at my local installation
and I try to use trackster to display a simple BED file, but it
invariably complains about not having a converter for this
datatype and it tells me to check my datatypes_conf.xml which I
did (not sure what I should be looking for, but this is the
section on BED files...

Am I missing a converter? And why would a BED file even needed to
be converted?

Thanks

Thon


  
  
  
  
  
  
  
  
  


  





  

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Re: [galaxy-dev] Troubleshooting file uploads (to Data Library)

[Hans-Rudolf Hotz]

Hi Clare

a few points to start:

 - do you define the 'File Format'?
   (don't use 'Auto-detect' for big files)

 - and similar to a recent question on the list: check your proxy
   settings


Regards, Hans-Rudof


On 08/21/2013 09:09 AM, Clare Sloggett wrote:


Sorry, missed some information: there are a handful of files, 35MB
(gzipped) each. The issue occurs even if I only try to upload one of
them though. The server is a 16-core machine.


On 21 August 2013 17:08, Clare Sloggett mailto:s...@unimelb.edu.au>> wrote:

Hi,

I am having trouble uploading files to a Data Library, and I'm not
sure where to begin troubleshooting. I'm uploading from a URL (but I
had a similar issue from the desktop). The symptom is that the
datasets in the library have the message "This job is queued" and
never seem to progress.

I am one of very few users of this instance (quite likely the only
user right this moment). I don't think the server is busy, so I'm
not sure why the files uploads don't seem to be proceeding. How can
I investigate further?

Thanks,
Clare

--

Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357  M: 0414 854 759




--

Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357  M: 0414 854 759


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Re: [galaxy-dev] Galaxy Release Cycle Length

[Hans-Rudolf Hotz]

Hi Dave

two months is a good time between releases.

Much more important than the release cycle length is fixing identified 
bugs on the release branch as well.


Regards, Hans-Rudolf



On 08/20/2013 08:36 PM, Dave Clements wrote:

Hello all,

At one of the GCC2013 Birds of a Feather sessions
 the
group was very clear that they would like to see less frequent releases
of Galaxy.  We're currently aiming to do a release every 2 months and
have been pretty successful at making that target.  In the past, we have
tried doing releases more often and less often.

Is there a sweet spot for the time between releases?

Please reply to the group.  We are interested in a discussion.

Thanks,

Dave C

--
http://galaxyproject.org/GCC2013
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/


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Re: [galaxy-dev] Passing user_email to a data source

[Hans-Rudolf Hotz]

Hi Anthony

I doubt it will solve your problem, but just as a general hint: you can 
use the email address for filtering. In our case, the user gets a 
different list of groups he/she can select from, eg:






		value="$__user_email__" column="0"/>




and our file '~/tool-data/access_to_miseq' looks like:

1...@fmi.ch gbioinfo
1...@fmi.ch gfungen
1...@fmi.ch gmeier
#   #
a...@fmi.ch gfungen
#   #
1...@fmi.ch gfungen
1...@fmi.ch gmeier




Regards, Hans-Rudolf



On 08/20/2013 05:51 PM, Anthony Bretaudeau wrote:

Hello,
I'm trying to add a new data source to my Galaxy instance, using
synchronous data depositing.
The data source needs to know the email address of the user who tries to
import data to the Galaxy server. I would have like to write something
like that:

 https://example.com/my/data/source";
check_values="false" method="get">
 Browse the XX data source $GALAXY_URL
 
 

Then Galaxy would have generated this url:
https://example.com/my/data/source?GALAXY_URL=http&user_email=t...@example.com


But this doesn't work, because the $__user_email__ seems to be available
only in  tag. I end up with this url which is useless:

https://example.com/my/data/source?GALAXY_URL=http&user_email=$__user_email__


Is there any way to do what I need to do? It would be great if variables
were available in  tags too.
Otherwise, maybe I could write a custom tool type to do this. Is there
any guideline for this?

I have seen someone talking about that a few months ago, but with no
answer:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011258.html

Thanks for your help
Regards
Anthony Bretaudeau
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Re: [galaxy-dev] OSError: [Errno 5] Input/output error

[Hans-Rudolf Hotz]

Please keep all replies on the list by using "reply all"


I am not really a tool shed expert, hence I can only direct you to the 
wiki pages: http://wiki.galaxyproject.org/Tool%20Shed



Hans-Rudolf

On 08/20/2013 12:12 PM, Richard Kuo wrote:

Hello Hans-Rudolf,

I am wondering if the issue could have been caused by the tool shed? I
had been playing around with adding new tools via the tool shed just
before this happened. The sys admin has restored our Galaxy instance to
a previous time point before I did all this and it seems to be working
alright now. Is there any documentation of how the tool shed interacts
with the conf files within the galaxy folder?

Thank you!
Richard


On Mon, Aug 19, 2013 at 12:32 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Richard

this looks like a system error to me (and has nothing to do with the
galaxy server itself). Something is wrong with your disk? which
might also be the original reason why you got complaints about the
upload speed.

Sorry, I can't help you any further. I suggest you contact your sys
admin.


Regards, Hans-Rudolf



On 08/19/2013 01:07 PM, Richard Kuo wrote:

Hello,

I tried restarting my local Galaxy instance today bit it won't
start up
properly. I keep getting this message when I run "sh run.sh":

Traceback (most recent call last):
File

"/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/webapps/galaxy/__buildapp.py",
line 35, in app_factory
  app = UniverseApplication( global_conf = global_conf,
**kwargs )
File

"/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/app.py",
line 79, in __init__
  self.datatypes_registry.load___datatypes( self.config.root,
self.config.datatypes_config )
File

"/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/datatypes/registry.__py",
line 273, in load_datatypes
  self.to_xml_file()
File

"/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/datatypes/registry.__py",
line 681, in to_xml_file
  os.close( fd )
OSError: [Errno 5] Input/output error


The reason for my restart was dur to a users complaint about
upload speeds.

Any help is much appreciated!
Richard


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Re: [galaxy-dev] upload file not functioning in local installation galaxy

[Hans-Rudolf Hotz]

Hi

One of our development boxes is (unfortunately) behind a different 
firewall, compared to the the other servers.


We fixed the problem (ie "Get Data -> Upload File -> choose file.  It is 
not uploading at all") by setting a proxy server. This could be done eg. 
by adding the following lines to "run.sh":


http_proxy=http://**.fmi.ch:
export http_proxy

Obviously, this solved other problems as well, like "Get Data -> UCSC"


Regards, Hans-Rudolf

On 08/19/2013 04:01 PM, Yinan Wan wrote:

Hi Hans-Rudolf,

Thanks for your reply.  But do you have any idea what might be related
with this "proxy issue"? What is required to open/set for galaxy to run?
Or do you might share your experience of how you solve the problem?

Thanks,
Yinan


On Mon, Aug 19, 2013 at 3:16 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Yinan

It might be unrelated, but we had a similar issue. The problem was
due to the proxy settings of our server.


Regards, Hans-Rudolf


On 08/16/2013 08:23 PM, Yinan Wan wrote:

Hi,

I have installed galaxy on our local server, when I was trying
to upload
data from:
Get Data -> Upload File -> choose file.  It is not uploading at
all; but
it works fine when using the URL option.  I wonder do you have any
suggestions about this problem?

The output from the command line is pasted below:
>
128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET
/api/histories/__5969b1f7201f12ae/contents?ids=__f09437b8822035f7 
HTTP/1.1"
200 - "http://128.118.201.68:8080/__history
<http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET
/api/histories/__5969b1f7201f12ae HTTP/1.1" 200 -
"http://128.118.201.68:8080/__history
<http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh;
Intel Mac
OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET
/api/histories/__5969b1f7201f12ae/contents?ids=__f09437b8822035f7 
HTTP/1.1"
200 - "http://128.118.201.68:8080/__history
<http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET
/api/users/current
HTTP/1.1" 200 - "http://128.118.201.68:8080/"; "Mozilla/5.0
(Macintosh;
Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 -
"http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac
OS X
10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST
/tool_runner/upload_async___create HTTP/1.1" 200 -
"http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac
OS X
10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET
/tool_runner/upload_async___message HTTP/1.1" 200 -
"http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac
OS X
10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history
HTTP/1.1"
200 - "http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh;
Intel Mac
OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95
Safari/537.36"
==>

   Thanks,
Yinan


--
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University


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Re: [galaxy-dev] OSError: [Errno 5] Input/output error

[Hans-Rudolf Hotz]

Hi Richard

this looks like a system error to me (and has nothing to do with the 
galaxy server itself). Something is wrong with your disk? which might 
also be the original reason why you got complaints about the upload speed.


Sorry, I can't help you any further. I suggest you contact your sys admin.


Regards, Hans-Rudolf


On 08/19/2013 01:07 PM, Richard Kuo wrote:

Hello,

I tried restarting my local Galaxy instance today bit it won't start up
properly. I keep getting this message when I run "sh run.sh":

Traceback (most recent call last):
   File
"/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
 app = UniverseApplication( global_conf = global_conf, **kwargs )
   File
"/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/app.py",
line 79, in __init__
 self.datatypes_registry.load_datatypes( self.config.root,
self.config.datatypes_config )
   File
"/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/datatypes/registry.py",
line 273, in load_datatypes
 self.to_xml_file()
   File
"/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/datatypes/registry.py",
line 681, in to_xml_file
 os.close( fd )
OSError: [Errno 5] Input/output error


The reason for my restart was dur to a users complaint about upload speeds.

Any help is much appreciated!
Richard


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Re: [galaxy-dev] upload file not functioning in local installation galaxy

[Hans-Rudolf Hotz]

Hi Yinan

It might be unrelated, but we had a similar issue. The problem was due 
to the proxy settings of our server.



Regards, Hans-Rudolf

On 08/16/2013 08:23 PM, Yinan Wan wrote:

Hi,

I have installed galaxy on our local server, when I was trying to upload
data from:
Get Data -> Upload File -> choose file.  It is not uploading at all; but
it works fine when using the URL option.  I wonder do you have any
suggestions about this problem?

The output from the command line is pasted below:
>
128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET
/api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1"
200 - "http://128.118.201.68:8080/history"; "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET
/api/histories/5969b1f7201f12ae HTTP/1.1" 200 -
"http://128.118.201.68:8080/history"; "Mozilla/5.0 (Macintosh; Intel Mac
OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET
/api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1"
200 - "http://128.118.201.68:8080/history"; "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/users/current
HTTP/1.1" 200 - "http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 -
"http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST
/tool_runner/upload_async_create HTTP/1.1" 200 -
"http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET
/tool_runner/upload_async_message HTTP/1.1" 200 -
"http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history HTTP/1.1"
200 - "http://128.118.201.68:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac
OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
Safari/537.36"
==>

  Thanks,
Yinan


--
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University


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Re: [galaxy-dev] Getting data from a database to create a dynamic combo box

[Hans-Rudolf Hotz]

Hi Ramon

You need to provide the code you have written and the error messages you 
get. Otherwise, it is very difficult for the community to help you.


Regards, Hans-Rudolf

On 08/16/2013 03:43 PM, Ramon Tiburski wrote:

I had tried a few things with this link, but I could not, I must be
doing something wrong.

 > Date: Fri, 16 Aug 2013 14:45:18 +0200
 > From: h...@fmi.ch
 > To: ramao_tiago_tibur...@hotmail.com
 > CC: galaxy-...@bx.psu.edu
 > Subject: Re: [galaxy-dev] Getting data from a database to create a
dynamic combo box
 >
 >
 >
 > On 08/16/2013 01:21 PM, Bjoern Gruening wrote:
 > > Hi,
 > >
 > > that can be tricky I guess.
 > > What you can always do is to write your own data_source application.
 > > Basically, you write your own small webpage with all the magic you need
 > > and only transfer the data you need. Like the UCSC genome browser.
 > >
 > > A really small example can be found here (without SQL):
 > >
https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/jmoleditor
 > >
 > > Hope that helps,
 > > Bjoern
 > >
 >
 > as an alternative, see this old e-mail thread
 >
 > http://tinyurl.com/6uom4uo
 >
 >
 > Regards, Hans-Rudolf
 >
 > >
 > >> Hi,
 > >> I need to create a combo box that will take data from a database
 > >> dynamically. How could I do this?
 > >>
 > >> Thank you
 > >>
 > >> ___
 > >> Please keep all replies on the list by using "reply all"
 > >> in your mail client. To manage your subscriptions to this
 > >> and other Galaxy lists, please use the interface at:
 > >> http://lists.bx.psu.edu/
 > >>
 > >> To search Galaxy mailing lists use the unified search at:
 > >> http://galaxyproject.org/search/mailinglists/
 > >
 > >
 > >
 > > ___
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 > > in your mail client. To manage your subscriptions to this
 > > and other Galaxy lists, please use the interface at:
 > > http://lists.bx.psu.edu/
 > >
 > > To search Galaxy mailing lists use the unified search at:
 > > http://galaxyproject.org/search/mailinglists/
 > >

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Re: [galaxy-dev] Getting data from a database to create a dynamic combo box

[Hans-Rudolf Hotz]

On 08/16/2013 01:21 PM, Bjoern Gruening wrote:

Hi,

that can be tricky I guess.
What you can always do is to write your own data_source application.
Basically, you write your own small webpage with all the magic you need
and only transfer the data you need. Like the UCSC genome browser.

A really small example can be found here (without SQL):
https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/jmoleditor

Hope that helps,
Bjoern



as an alternative, see this old e-mail thread

http://tinyurl.com/6uom4uo


Regards, Hans-Rudolf




Hi,
I need to create a combo box that will take data from a database
dynamically. How could I do this?

Thank you

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Re: [galaxy-dev] getting large files into a local instance of Galaxy

[Hans-Rudolf Hotz]

Hi Gerald

Have you looked into 'Data Libraries'?

http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

This will allow you to access the files without data duplication.

Regards, Hans-Rudolf


On 08/05/2013 08:48 PM, Gerald Bothe wrote:

Trying out a local instance of Galaxy. Small files can be uploaded with
"browse.." but this works only for files under 2Gb. Is there a folder in
a local copy of galaxy-dist where I can copy a large file and have it
show up in the Get Data/Upload File/Files uploaded via FTP window so
that I can properly get it into the local history? Copying it directly
into the database seemed not to work, it didn't show up anywhere.
Gerald

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Re: [galaxy-dev] Mail is not configured for this Galaxy instance.

[Hans-Rudolf Hotz]

On 08/06/2013 08:17 AM, shenwiyn wrote:

Hi Hans-Rudolf,
Thank you very much for you help.Actually I want some more information
about how to configure 'smtp_server' in "universe_wsgi.ini".Could you
show me some samples to have a look please?



you need the address of your smtp server, eg:

smtp_server = abcd.fmi.ch





Regards, shenwiyn
*From:* Hans-Rudolf Hotz <mailto:h...@fmi.ch>
*Date:* 2013-07-31 23:40
*To:* shenwiyn <mailto:shenw...@gmail.com>
*CC:* galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
*Subject:* Re: [galaxy-dev] Mail is not configured for this Galaxy instance.
Hi Shenwiyn
You need to specify a SMTP server. Have a look at the 'smtp_server'
settings in your "universe_wsgi.ini" file.
Regards, Hans-Rudolf
On 07/31/2013 04:19 PM, shenwiyn wrote:
 > Hi everyone,
 > In my local Galaxy,when I want to reset my Login password,some error
 > occurre
 > :"Mail is not configured for this Galaxy instance. Please contact an 
administrator.
 > "Could anyone tell me some imformation about how to configure the mail
 > for my Galaxy instance?
 > Thank you very much.
 > 
 > shenwiyn
 >
 >
 > ___
 > Please keep all replies on the list by using "reply all"
 > in your mail client.  To manage your subscriptions to this
 > and other Galaxy lists, please use the interface at:
 >http://lists.bx.psu.edu/
 >
 > To search Galaxy mailing lists use the unified search at:
 >http://galaxyproject.org/search/mailinglists/
 >

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Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

[Hans-Rudolf Hotz]

and now, what happens, if you change it to 'tabular'?

(click on the pencil icon - 'Edit Attributes', and then on Datatype



On 08/02/2013 12:18 PM, Nikhil Mallela wrote:

Hi Hans-Rudolf,

I was wrong previously. It is output produced (.txt) while computing the
quality statistics on the .qual file
The output format seems to have been detected by Galaxy as a ".txt" file.

Here is a snapshot.

Inline image 1

Nikhil.

On Fri, Aug 2, 2013 at 11:58 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi

I guess, you misunderstood my question. I was revering to the format
within galaxy, ie what is written in the preview window
(unfortunately, you did cut this off from your pictures in your
original post) between "format:" and ", database".


Hans-Rudolf


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Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

[Hans-Rudolf Hotz]

Hi

I guess, you misunderstood my question. I was revering to the format 
within galaxy, ie what is written in the preview window (unfortunately, 
you did cut this off from your pictures in your original post) between 
"format:" and ", database".



Hans-Rudolf

On 08/02/2013 11:50 AM, Nikhil Mallela wrote:

Hi Hans-Rudolf,

The data format is ".qual" file from SOLiD sequencers.
Its the same sample file that I've uploaded to the main and the localFormat
installation.
But as you have seen in my previous post, the headers are inline with
the data on main; but not on my local installation.
what could be the reason ?

Thanks,
Nikhil.

On Fri, Aug 2, 2013 at 11:21 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Nikhil

what is the data format for this data set in your local installation
and on main?

Regards, Hans-Rudolf




On 08/02/2013 09:56 AM, Nikhil Mallela wrote:


Hi,

A few days ago, I have installed the stable release of of Galaxy
local
instanceon my Workstation & I am running it behind Apache web
server proxy .

In regard to the data snapshots, I've observed that, it is much more
organized on the Galaxy main rather than on my local instance.
For example, Take a look at these pictures:

On my local instance:
Inline image 1

On the Galaxy main: (also, this Inline image 4 is missing on my
local
instance)
Inline image 2

Also, when I click the view Inline image 3 on my local instance,the

headers of the data is not corresponding to its respective columns.
So, how can I fine tune these ?

Thanks in advance!
Nikhil.


--

--__--
Nikhil Vinod Mallela, M.Sc.
University of Muenster,
Institute of Bioinformatics,
Neil-Stensen Str. 12-14,
48149, Muenster,Germany.

Tel.:+49 0251 83 50006
Fax: +49 0251 83 53005
Email: mall...@uni-muenster.de <mailto:mall...@uni-muenster.de>
  <mailto:mallela@uni-muenster.__de
<mailto:mall...@uni-muenster.de>>
http://complex-systems.uni-__muenster.de/
<http://complex-systems.uni-muenster.de/>
--__--



_
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<http://galaxyproject.org/search/mailinglists/>




--


Nikhil Vinod Mallela, M.Sc.
University of Muenster,
Institute of Bioinformatics,
Neil-Stensen Str. 12-14,
48149, Muenster,Germany.

Tel.:+49 0251 83 50006
Fax: +49 0251 83 53005
Email:  mall...@uni-muenster.de  <mailto:mall...@uni-muenster.de>
http://complex-systems.uni-muenster.de/



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Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

[Hans-Rudolf Hotz]

Hi Nikhil

what is the data format for this data set in your local installation and 
on main?


Regards, Hans-Rudolf



On 08/02/2013 09:56 AM, Nikhil Mallela wrote:


Hi,

A few days ago, I have installed the stable release of of Galaxy local
instanceon my Workstation & I am running it behind Apache web server proxy .
In regard to the data snapshots, I've observed that, it is much more
organized on the Galaxy main rather than on my local instance.
For example, Take a look at these pictures:

On my local instance:
Inline image 1

On the Galaxy main: (also, this Inline image 4 is missing on my local
instance)
Inline image 2

Also, when I click the view Inline image 3 on my local instance,the
headers of the data is not corresponding to its respective columns.
So, how can I fine tune these ?

Thanks in advance!
Nikhil.


--


Nikhil Vinod Mallela, M.Sc.
University of Muenster,
Institute of Bioinformatics,
Neil-Stensen Str. 12-14,
48149, Muenster,Germany.

Tel.:+49 0251 83 50006
Fax: +49 0251 83 53005
Email:  mall...@uni-muenster.de  
http://complex-systems.uni-muenster.de/




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Re: [galaxy-dev] Mail is not configured for this Galaxy instance.

[Hans-Rudolf Hotz]

Hi Shenwiyn

You need to specify a SMTP server. Have a look at the 'smtp_server' 
settings in your "universe_wsgi.ini" file.



Regards, Hans-Rudolf




On 07/31/2013 04:19 PM, shenwiyn wrote:

Hi everyone,
In my local Galaxy,when I want to reset my Login password,some error
occurre
:"Mail is not configured for this Galaxy instance. Please contact an 
administrator.
"Could anyone tell me some imformation about how to configure the mail
for my Galaxy instance?
Thank you very much.

shenwiyn


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Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome

[Hans-Rudolf Hotz]

Hi Moritz


I am not a galaxy tool shed expert, but I recommend you start with 
reading these wiki pages:


http://wiki.galaxyproject.org/Tool%20Shed

http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy


and then try installing BWA via the tool shed and ask (if any) specific 
questions (preferably with a new subject line) on the mailing list.



Regards  Hans-Rudolf


On 07/22/2013 11:20 AM, Moritz Juchler wrote:

Hey,

with the "tool file" line I got it working :)
Thanks a lot. Could you answer the question regarding Tool Shed: "If I
would use Tool Shed, could I skip all these manual steps? Is the
installation of BWA with Tool Shed also this complicated or is it more
simle?"

Best
Moritz


On 17 July 2013 09:51, Moritz Juchler mailto:juch...@stud.uni-heidelberg.de>> wrote:

Hey,

no thats correct I did not use Tool Shed. If I would use it, could I
skip all these manual steps? Is the installation of BWA with Tool
Shed also this complicated or is it more simle?

How did you not follow my steps :) I wrote down everything clearly,
at least thats what I was hoping.

And no I didnt write this line " " Thats the first time, I am
seeing this tutorial :( I will try this out right now

Best
Moritz


    On 17 July 2013 09:42, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Moritz

I am struggling to follow what exactly you have done. As far as
I can see, you did not use the toolshed
(http://wiki.galaxyproject.__org/Tool%20Shed
<http://wiki.galaxyproject.org/Tool%20Shed>) to install the BWA
alinger tool, but did all manually?

If so, have you added the following line:

  

to the "tool_conf.xml" file, and restarted Galaxy?


see also:
http://wiki.galaxyproject.org/__Admin/Tools/Add%20Tool%__20Tutorial
<http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial>



Hope this helps
Hans-Rudolf





On 07/16/2013 08:35 PM, Moritz Juchler wrote:

Hello Ladies and Gentlemen,

I am Moritz Juchler from University Heidelberg. For my
Bachelor thesis I
have to choose a bioinformatic pipeline management tool to
find SNP's in
genomes from hcc patients. My decision was made in favor of
galaxy. I
have a 64-bit openSuse 11.3 server.
I have installed Galaxy locally, since we have a) very large
files
(>30GB per patient) and b) the data is protection sensitive.
I kept
close to http://wiki.galaxyproject.org/__Admin/Get%20Galaxy
<http://wiki.galaxyproject.org/Admin/Get%20Galaxy>
Now I would like to run this bpipe pipeline:
http://pastebin.com/sZd5vfdL
And the first step is to align my genome to a _hg19
reference genome_

which I have locally under /genedata/human_genome_GRCh37/__.

 trr@portalmoritz:~> ls -l /genedata/human_genome_GRCh37/
 total 8486312
 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa
 -rw-r--r-- 1 trr root   8591 2013-07-01 16:06
hg19.fa.amb
 -rw-r--r-- 1 trr root   4040 2013-07-01 16:06
hg19.fa.ann
 -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05
hg19.fa.bwt
 -rw-r--r-- 1 trr root  784290318 2013-07-01 16:06
hg19.fa.pac
 -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31
hg19.fa.sa <http://hg19.fa.sa>
 <http://hg19.fa.sa>


_bwa is installed and gives me:_


 trr@portalmoritz:~> bwa
 Program: bwa (alignment via Burrows-Wheeler transformation)
 Version: 0.7.5a-r405
 Contact: Heng Li mailto:l...@sanger.ac.uk> <mailto:l...@sanger.ac.uk
<mailto:l...@sanger.ac.uk>>>



Then I tried to follow this guide:
http://wiki.galaxyproject.org/__Admin/NGS%20Local%20Setup
<http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup> to
get the
reference files and
http://wiki.galaxyproject.org/__Admin/Config/Tool%__20Dependencies
<http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies>.

This is my _$PATH_


 trr@portalmoritz:~> echo $PATH


/home/trr/bin:/usr/local/bin:/__usr/bin:/bin:/usr/bin/X11:/__usr/X11R6/bin:/usr/games:/__home/trr/bpipe-0.9.8/bin:/__home/trr/bwa-0.7.5a:/home/trr/__samtools-0.1.19


_In the universe_wsgi.ini I changed:_


 tool_dependency_dir =
/home/trr/galaxy-dist/tool___depe

Re: [galaxy-dev] Galaxy Local Admin user

[Hans-Rudolf Hotz]

Hi Chadi

I am not familiar with the this tool

I recommend to try running the tool manually on the command line first, 
and then post the error on the mailing list (with a new subject) IF the 
error has something to do with Galaxy.


Hans-Rudolf


On 07/17/2013 05:00 PM, Chadi Abdul Kader El Farran wrote:

Dear Hans-Rudolf,

Thank you for your reply once again.

It appears that the problem is from a tool I installed in Galaxy.  It is called 
ngsplot.

Whenever I try to do any analysis, I get the following error:

"Traceback (most recent call last):
   File "/home/swarna/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 94, 
in queue_job
 job_wrapper.finish( stdout, stderr, exit_code )
   File "/home/swarna/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1009, in 
finish
 self.sa_session.flush()
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
 line 114, in do
 return getattr(self.registry(), name)(*args, **kwargs)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
 line 1718, in flush
 self._flush(objects)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
 line 1789, in _flush
 flush_context.execute()
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
 line 331, in execute
 rec.execute(self)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
 line 475, in execute
 uow
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
 line 59, in save_obj
 mapper, table, update)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
 line 485, in _emit_update_statements
 execute(statement, params)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 1449, in execute
 params)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 1584, in _execute_clauseelement
 compiled_sql, distilled_params
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 1698, in _execute_context
 context)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
 line 1691, in _execute_context
 context)
   File 
"/home/swarna/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
 line 331, in do_execute
 cursor.execute(statement, parameters)
ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless 
you use a text_factory that can interpret 8-bit bytestrings (like text_factory 
= str). It is highly recommended that you instead just switch your application 
to Unicode strings. u'UPDATE job SET update_time=?, stdout=?, stderr=? WHERE 
job.id = ?' ('2013-07-17 14:56:30.112896', '\nzip error: Nothing to do! 
(data.zip)\n', 'mv: cannot stat \xe2\x80\x98data.zip\xe2\x80\x99: No such file 
or directory\n', 41)
Tool execution generated the following error message:
Unable to finish job"

Can you kindly help me?

With warmest regards,

Chadi EL Farran (Post Graduate Student)
Dr. Jonathan Yuin-Han LOH's Laboratory
#08-01, Institute of Molecular and Cell Biology (IMCB)
61 Biopolis Drive, Proteos
Singapore 138673
Contact No: +65-91944793
E-mail: ch...@nus.edu.sg

From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, July 17, 2013 3:54 PM
To: Chadi Abdul Kader El Farran
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy Local Admin user

Please keep all replies on the list by using "reply all"  !

for my reply see below...

On 07/17/2013 06:58 AM, Chadi Abdul Kader El Farran wrote:

Dear Hans-Rudolf,

Thank you for your reply.

The problem was solved by restarting.

Now my problem is that I am unable to upload files into my Galaxy.

I have put the following code in Universe_wsgi.ini:

"# Directories of files contained in the following directory can be uploaded to 
a library from the Admin view
library_import_dir = /upload"

However when I upload files to a data library, all files will seem to have no 
information (0 bytes)



That is very crypticand you need to provide more details

   - did you get an error?
   - how do you know the files are empty
   - what happens if you work with the files


make sure to follow the wiki page:

http://wiki.galaxyproject.org/Admin/DataLibraries/Librarie