Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3

[Leon Mei]

Hi Nate,

Thanks for the suggestion! Unfortunately, it still failed :(

I got the following error message in proftp log:

2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres
cmd_escapestring
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_open
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is
now 2
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_open
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_close
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is
now 1
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_close
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres
cmd_escapestring
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cache hit for user '
hailiang.m...@nbic.nl'
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: >>> cmd_check
2013-08-09 08:32:41,777 mod_sql/4.3[32384]: checking password using
SQLAuthType 'sha1'
2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha1' SQLAuthType handler
reports failure
2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using
SQLAuthType 'sha256'
2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha256' SQLAuthType handler
reports failure
2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using
SQLAuthType 'pbkdf2'
2013-08-09 08:32:41,841 mod_sql/4.3[32384]: 'pbkdf2' SQLAuthType handler
reports failure
2013-08-09 08:32:41,841 mod_sql/4.3[32384]: <<< cmd_check
2013-08-09 08:32:41,841 mod_sql/4.3[32384]: <<< cmd_auth

The old user account generated before our code update still works.

I wonder how it is configured at the Galaxy main server?

Thanks,
Leon



On Thu, Aug 8, 2013 at 8:45 PM, Nate Coraor  wrote:

> On Jul 26, 2013, at 3:51 PM, Leon Mei wrote:
>
> > Dear galaxy developers,
> >
> > We have tried today to upgrade our proftpd configuration to make
> uploading for our galaxy users possible again, both for users with "old" as
> well as "new" style hashed passwords. We upgraded proftpd on the server to
> 1.3.5rc3 and have the following SQL part in our configuration file based on
> the post of
> http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html
> >
> > SQLEngine   on
> > SQLLogFile  /var/log/proftpd-sql.log
> > SQLBackend  postgres
> > SQLConnectInfo  galaxy@localhost:5840 galaxyftp <[ourpassword]>
> > SQLAuthTypesSHA1 SHA256 PBKDF2
> > SQLPasswordPBKDF2 SHA256 1000 24
> > SQLPasswordUserSalt   sql:/GetUserSalt
> > SQLAuthenticate users
> > SQLDefaultUID   108
> > SQLDefaultGID   116
> > SQLDefaultHomedir   /opt/cloudman/pkg/proftpd/var
> > SQLUserInfo custom:/LookupGalaxyUser
> > SQLNamedQuery  LookupGalaxyUser  SELECT "email, (CASE WHEN
> substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38
> for 32) ELSE password END) AS
> password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM
> galaxy_user WHERE email='%U'"
> > SQLNamedQuery  GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1
> for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt
> FROM galaxy_user WHERE email='%U'"
> >
> > We have executed the LookupGalaxyUser and GetUserSalt commands manually,
> and the results look good. Now, old users can login via ftp, but for a new
> user, the authentication still fails:
> >
> > 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: >>> cmd_check
> > 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using
> SQLAuthType 'sha1'
> > 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler
> reports failure
> > 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using
> SQLAuthType 'pbkdf2'
> > 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler
> reports failure
> >
> > What are we missing?
> >
> > Thanks!
> >
> > Rob and Leon
>
> Hallo Leon and Rob,
>
> Thanks for working on this, when I'd looked a couple months ago I could
> not find an entirely-ProFTPD way to do this.  I think it may have actually
> come about because I asked about it on their IRC channel. ;)
>
> This may work if you change SQLPasswordPBKDF2:
>
>   SQLPasswordPBKDF2 SHA256 1 24
>
> It'd be great if ProFTPD also supported pulling those values dynamically
> from the database, but Galaxy's PBKDF2 code currently has them hardcoded,
> so they will be static anyway.
>
> --nate
>
> >
> >
> > --
> > Hailiang (Leon) Mei
> > Netherlands Bioinformatics Center
> > BioAssist NGS Taskforce
> >  - http://ngs.nbic.nl
> > Skype: leon_meiMobile: +31 6 41709231
> > ___
> > 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://galaxyproj

Re: [galaxy-dev] Galaxy on cloud config issues

[Ulyanov_Anatoly]

Hello Dannon,

This bucket did not launch Galaxy properly. Here is the whole Cluster status 
log:

22:11:22 - Master starting
22:11:23 - Completed initial cluster configuration. This seems to be a new 
cluster; waiting to configure the type
22:11:27 - SGE prerequisites OK; starting the service
22:11:35 - Configuring SGE...
22:11:45 - Successfully setup SGE; configuring SGE
22:11:46 - Saved file 'persistent_data.yaml' to bucket 
'cm-bcf1a9a44e022cfe983b8302199ed978'
22:11:46 - Saved file 'cm_boot.py' to bucket 
'cm-bcf1a9a44e022cfe983b8302199ed978'
22:11:47 - Saved file 'cm.tar.gz' to bucket 
'cm-bcf1a9a44e022cfe983b8302199ed978'
22:11:47 - Saved file 'EmptyGalaxy.clusterName' to bucket 
'cm-bcf1a9a44e022cfe983b8302199ed978'

The "Access Galaxy" button on CloudMan Console stays gray and  the Services 
Control panel on Admin Console  shows that Galaxy and PostgreSQL are not 
running. Maybe the log file gives you a clue:

'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version:  (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-08 22:11:22,729: Initializing app
[DEBUG] app:55 2013-08-08 22:11:22,729: Running on 'ec2' type of cloud.
[DEBUG] app:72 2013-08-08 22:11:22,729: Getting pd.yaml
[DEBUG] ec2:275 2013-08-08 22:11:22,730: No S3 Connection, creating a new one.
[DEBUG] ec2:278 2013-08-08 22:11:22,730: Got boto S3 connection.
[DEBUG] misc:113 2013-08-08 22:11:22,761: Checking if bucket 
'cm-bcf1a9a44e022cfe983b8302199ed978' exists... it does not.
[DEBUG] misc:444 2013-08-08 22:11:22,761: Bucket 
'cm-bcf1a9a44e022cfe983b8302199ed978' does not exist, did not get remote file 
'persistent_data.yaml'
...


Thank you.




Best Regards,
Anatoly

From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Wednesday, August 07, 2013 5:01 PM
To: Ulyanov_Anatoly
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues

A new tools volume will be released shortly.  For now, you can launch the 
previous cloudman release using the following:

https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop

On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly 
mailto:ulyanov_anat...@allergan.com>> wrote:
Hello,

Does anybody use the last Galaxy image? I am running Galaxy image on EC2:

Instance ID i-1b2d3773
Image ID (AMI) ami-118bfc78

It looks as those three tools have configuration problems:

EBOSS
Blast+
meme

For all three I am getting a message that looks  like that:

/mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found
Error invoking command: blastp

Is there a way to fix configuration files for those tools?

Thank you.

Best Regards,
Anatoly


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This e-mail, including any attachments, is meant only for the intended 
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Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

[Ravpreet Setia]

In the form, under "Instances in your account" I choose New Cluster.  Let me 
know if there are additional details you need.

From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent: Thursday, August 08, 2013 4:39 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

I tried this method again and it still does not work. The only items in /mnt 
are the directories cm and lost+found.

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 01, 2013 4:48 PM
To: Ravpreet Setia
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

The new volume update hasn't been released yet to fix those tool issues, but 
the existing volume should actually appear in /mnt at launch.


On Thu, Aug 1, 2013 at 4:28 PM, Ravpreet Setia 
mailto:ravpreet.se...@oicr.on.ca>> wrote:
Thanks for letting me know, my old credentials have been disabled.

Anyways, that is all the log contained. I clicked on "show all".  Does 
launching it with this method work on your end?

From: 
galaxy-dev-boun...@lists.bx.psu.edu 
[galaxy-dev-boun...@lists.bx.psu.edu]
 on behalf of Ravpreet Setia 
[ravpreet.se...@oicr.on.ca]
Sent: Thursday, August 01, 2013 4:11 PM
To: Dannon Baker

Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

Here it is:




'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version:  (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-01 20:07:40,138: Initializing app
[DEBUG] app:55 2013-08-01 20:07:40,138: Running on 'ec2' type of cloud.
[DEBUG] app:72 2013-08-01 20:07:40,138: Getting pd.yaml
[DEBUG] ec2:275 2013-08-01 20:07:40,138: No S3 Connection, creating a new one.
[DEBUG] ec2:278 2013-08-01 20:07:40,139: Got boto S3 connection.
[DEBUG] misc:113 2013-08-01 20:07:40,229: Checking if bucket 
'cm-35f4d40b627583b6949bc5de11bcfecc' exists... it does not.
[DEBUG] misc:444 2013-08-01 20:07:40,229: Bucket 
'cm-35f4d40b627583b6949bc5de11bcfecc' does not exist, did not get remote file 
'persistent_data.yaml'
[INFO] app:78 2013-08-01 20:07:40,229: Master starting
[DEBUG] master:70 2013-08-01 20:07:40,229: Initializing console manager - 
cluster start time: 2013-08-01 20:07:40.229549
[DEBUG] connection:648 2013-08-01 20:07:40,231: Start from server, version: 
8.0, properties: {u'platform': 'Erlang/OTP', u'product': 'RabbitMQ', 
u'version': '1.7.2', u'copyright': 'Copyright (C) 2007-2010 LShift Ltd., 
Cohesive Financial Technologies LLC., and Rabbit Technologies Ltd.', 
u'information': 'Licensed under the MPL.  See http://www.rabbitmq.com/'}, 
mechanisms: ['PLAIN', 'AMQPLAIN'], locales: ['en_US']
[DEBUG] connection:494 2013-08-01 20:07:40,263: Open OK! known_hosts 
[ip-10-179-15-41.ec2.internal:5672]
[DEBUG] channel:70 2013-08-01 20:07:40,263: using channel_id: 1
[DEBUG] channel:484 2013-08-01 20:07:40,264: Channel open
[DEBUG] comm:35 2013-08-01 20:07:40,266: Successfully established AMQP 
connection
[DEBUG] master:510 2013-08-01 20:07:40,266: Trying to discover any worker 
instances associated with this cluster...
[DEBUG] ec2:246 2013-08-01 20:07:40,267: Establishing boto EC2 connection
[DEBUG] ec2:103 2013-08-01 20:07:40,267: Gathering instance zone, attempt 0
[DEBUG] ec2:108 2013-08-01 20:07:40,270: Instance zone is 'us-east-1d'
[DEBUG] ec2:263 2013-08-01 20:07:40,516: Got boto EC2 connection for region 
'us-east-1'
[DEBUG] ec2:66 2013-08-01 20:07:40,574: Gathering instance id, attempt 0
[DEBUG] ec2:71 2013-08-01 20:07:40,575: Instance ID is 'i-7b386714'
[DEBUG] ec2:295 2013-08-01 20:07:40,639: Adding tag 
'clusterName:gal_oldami_form2' to resource 'i-7b386714'
[DEBUG] ec2:295 2013-08-01 20:07:41,066: Adding tag 'role:master' to resource 
'i-7b386714'
[DEBUG] master:174 2013-08-01 20:07:41,223: ud at manager start: {'access_key': 
'AKIAIUSCRANAJESP3GFQ', 'cloudman_home': '/mnt/cm', 'cluster_name': 
'gal_oldami_form2', 'bucket_default': 'gxy-workshop', 'boot_script_name': 
'cm_boot.py', 'bucket_cluster': 'cm-35f4d40b627583b6949bc5de11bcfecc', 
'boot_script_path': '/tmp/cm', 'role': 'master', 'secret_key': 
'EV12T4PMGSbM1IZmS7ZUJVi9nCvMncnrxXvytacJ', 'password': 'google'}
[DEBUG] pss:25 2013-08-01 20:07:41,224: Configured PSS as master
[DEBUG] master:204 2013-08-01 20:07:41,225: Cheking for and adding any 
preconfigured services
[DEBUG] master:529 2013-08-01 20:07:41,225: Trying to discover any volumes 
attached to this instance...
[DEBUG] base:55 2013-08-01 20:07:41,236: Enabling 'root' controller, class: CM
[DEBUG] bui

Re: [galaxy-dev] Galaxy on cloud config issues

[Ravpreet Setia]

Initially Anatoly and I had the problem with the symlinks and were prescribed 
the link to launch the old ami as a temporary solution until the latest ami 
gets fixed. Thus I was curious if Anatoly would experience the same issue as me 
when launching the older ami this way.

Anyways, I'll continue the discussion on the other thread. Thanks!

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 08, 2013 5:08 PM
To: Ravpreet Setia
Cc: Ulyanov_Anatoly; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues

On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia 
mailto:ravpreet.se...@oicr.on.ca>> wrote:
Yeah, nothing happens after SGE gets to the running state. The directory 
structure of the old ami does not appear in /mnt. The log was posted in the 
following thread:

Ahh, ok - I assumed since there was no further reply that the workaround worked 
for you.  I'll take another look at your log, but if you could follow up (on 
that other thread) with some more details about your cluster that'd be great.  
Specifically, how you're launching it, if it's an old cluster being relaunched, 
a share_string-based new cluster, etc.

Additionally, I am not sure what you mean by, "This will not be the same issue 
as the tool volume update.".

If your volume isn't even mounting, then it has nothing to do with the symlinks 
referred to by Ulyanov.  His volume mounts, it's just not completely functional.
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Re: [galaxy-dev] Galaxy on cloud config issues

[Dannon Baker]

On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia wrote:

>  Yeah, nothing happens after SGE gets to the running state. The directory
> structure of the old ami does not appear in /mnt. The log was posted in the
> following thread:
>

Ahh, ok - I assumed since there was no further reply that the workaround
worked for you.  I'll take another look at your log, but if you could
follow up (on that other thread) with some more details about your cluster
that'd be great.  Specifically, how you're launching it, if it's an old
cluster being relaunched, a share_string-based new cluster, etc.

Additionally, I am not sure what you mean by, "This will not be the same
> issue as the tool volume update.".
>

If your volume isn't even mounting, then it has nothing to do with the
symlinks referred to by Ulyanov.  His volume mounts, it's just not
completely functional.
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Re: [galaxy-dev] Galaxy on cloud config issues

[Ravpreet Setia]

Yeah, nothing happens after SGE gets to the running state. The directory 
structure of the old ami does not appear in /mnt. The log was posted in the 
following thread:

"Cloudman - When will the symlinks be resolved ?"

Additionally, I am not sure what you mean by, "This will not be the same issue 
as the tool volume update.".

Thanks



From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 08, 2013 4:40 PM
To: Ravpreet Setia
Cc: Ulyanov_Anatoly; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues

Ravpreet -- can you provide details as to what's failing for you?

If I remember correctly, you had an odd issue where nothing was actually 
appearing at /mnt, right?  This will not be the same issue as the tool volume 
update.


On Thu, Aug 8, 2013 at 4:36 PM, Ravpreet Setia 
mailto:ravpreet.se...@oicr.on.ca>> wrote:
Anatoly, did this method work for you? It is not working for me.

From: 
galaxy-dev-boun...@lists.bx.psu.edu 
[galaxy-dev-boun...@lists.bx.psu.edu]
 on behalf of Dannon Baker 
[dannon.ba...@gmail.com]
Sent: Wednesday, August 07, 2013 8:00 PM
To: Ulyanov_Anatoly
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues

A new tools volume will be released shortly.  For now, you can launch the 
previous cloudman release using the following:

https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop


On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly 
mailto:ulyanov_anat...@allergan.com>> wrote:
Hello,

Does anybody use the last Galaxy image? I am running Galaxy image on EC2:

Instance ID i-1b2d3773
Image ID (AMI) ami-118bfc78

It looks as those three tools have configuration problems:

EBOSS
Blast+
meme

For all three I am getting a message that looks  like that:

/mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found
Error invoking command: blastp

Is there a way to fix configuration files for those tools?

Thank you.

Best Regards,
Anatoly


This e-mail, including any attachments, is meant only for the intended 
recipient and may be a confidential communication or a communication privileged 
by law. If you received this e-mail in error, any review, use, dissemination, 
distribution, or copying of this e-mail is strictly prohibited. Please notify 
the sender immediately of the error by return e-mail and please delete this 
message from your system. Thank you in advance for your cooperation.

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Re: [galaxy-dev] Galaxy on cloud config issues

[Dannon Baker]

Ravpreet -- can you provide details as to what's failing for you?

If I remember correctly, you had an odd issue where nothing was actually
appearing at /mnt, right?  This will not be the same issue as the tool
volume update.


On Thu, Aug 8, 2013 at 4:36 PM, Ravpreet Setia wrote:

>  Anatoly, did this method work for you? It is not working for me.
>  --
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [
> galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Dannon Baker [
> dannon.ba...@gmail.com]
> *Sent:* Wednesday, August 07, 2013 8:00 PM
> *To:* Ulyanov_Anatoly
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] Galaxy on cloud config issues
>
>   A new tools volume will be released shortly.  For now, you can launch
> the previous cloudman release using the following:
>
>
> https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop
>
>
> On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <
> ulyanov_anat...@allergan.com> wrote:
>
>>  Hello,
>>
>> ** **
>>
>> Does anybody use the last Galaxy image? I am running Galaxy image on EC2:
>> 
>>
>> ** **
>>
>> Instance ID i-1b2d3773
>>
>> Image ID (AMI) ami-118bfc78 
>>
>> ** **
>>
>> It looks as those three tools have configuration problems:
>>
>> ** **
>>
>> EBOSS
>>
>> Blast+
>>
>> meme
>>
>> ** **
>>
>> For all three I am getting a message that looks  like that:
>>
>> ** **
>>
>> /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found
>> 
>>
>> Error invoking command: blastp
>>
>> ** **
>>
>> Is there a way to fix configuration files for those tools?
>>
>> ** **
>>
>> Thank you.
>>
>> ** **
>>
>> Best Regards,
>>
>> Anatoly
>>
>> ** **
>>
>> This e-mail, including any attachments, is meant only for the intended
>> recipient and may be a confidential communication or a communication
>> privileged by law. If you received this e-mail in error, any review, use,
>> dissemination, distribution, or copying of this e-mail is strictly
>> prohibited. Please notify the sender immediately of the error by return
>> e-mail and please delete this message from your system. Thank you in
>> advance for your cooperation.
>>
>> ___
>> 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] Galaxy on cloud config issues

[Ravpreet Setia]

Anatoly, did this method work for you? It is not working for me.

From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Dannon Baker [dannon.ba...@gmail.com]
Sent: Wednesday, August 07, 2013 8:00 PM
To: Ulyanov_Anatoly
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues

A new tools volume will be released shortly.  For now, you can launch the 
previous cloudman release using the following:

https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop


On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly 
mailto:ulyanov_anat...@allergan.com>> wrote:
Hello,

Does anybody use the last Galaxy image? I am running Galaxy image on EC2:

Instance ID i-1b2d3773
Image ID (AMI) ami-118bfc78

It looks as those three tools have configuration problems:

EBOSS
Blast+
meme

For all three I am getting a message that looks  like that:

/mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found
Error invoking command: blastp

Is there a way to fix configuration files for those tools?

Thank you.

Best Regards,
Anatoly


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Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

[Ravpreet Setia]

I tried this method again and it still does not work. The only items in /mnt 
are the directories cm and lost+found.

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 01, 2013 4:48 PM
To: Ravpreet Setia
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

The new volume update hasn't been released yet to fix those tool issues, but 
the existing volume should actually appear in /mnt at launch.


On Thu, Aug 1, 2013 at 4:28 PM, Ravpreet Setia 
mailto:ravpreet.se...@oicr.on.ca>> wrote:
Thanks for letting me know, my old credentials have been disabled.

Anyways, that is all the log contained. I clicked on "show all".  Does 
launching it with this method work on your end?

From: 
galaxy-dev-boun...@lists.bx.psu.edu 
[galaxy-dev-boun...@lists.bx.psu.edu]
 on behalf of Ravpreet Setia 
[ravpreet.se...@oicr.on.ca]
Sent: Thursday, August 01, 2013 4:11 PM
To: Dannon Baker

Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?

Here it is:




'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version:  (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-01 20:07:40,138: Initializing app
[DEBUG] app:55 2013-08-01 20:07:40,138: Running on 'ec2' type of cloud.
[DEBUG] app:72 2013-08-01 20:07:40,138: Getting pd.yaml
[DEBUG] ec2:275 2013-08-01 20:07:40,138: No S3 Connection, creating a new one.
[DEBUG] ec2:278 2013-08-01 20:07:40,139: Got boto S3 connection.
[DEBUG] misc:113 2013-08-01 20:07:40,229: Checking if bucket 
'cm-35f4d40b627583b6949bc5de11bcfecc' exists... it does not.
[DEBUG] misc:444 2013-08-01 20:07:40,229: Bucket 
'cm-35f4d40b627583b6949bc5de11bcfecc' does not exist, did not get remote file 
'persistent_data.yaml'
[INFO] app:78 2013-08-01 20:07:40,229: Master starting
[DEBUG] master:70 2013-08-01 20:07:40,229: Initializing console manager - 
cluster start time: 2013-08-01 20:07:40.229549
[DEBUG] connection:648 2013-08-01 20:07:40,231: Start from server, version: 
8.0, properties: {u'platform': 'Erlang/OTP', u'product': 'RabbitMQ', 
u'version': '1.7.2', u'copyright': 'Copyright (C) 2007-2010 LShift Ltd., 
Cohesive Financial Technologies LLC., and Rabbit Technologies Ltd.', 
u'information': 'Licensed under the MPL.  See http://www.rabbitmq.com/'}, 
mechanisms: ['PLAIN', 'AMQPLAIN'], locales: ['en_US']
[DEBUG] connection:494 2013-08-01 20:07:40,263: Open OK! known_hosts 
[ip-10-179-15-41.ec2.internal:5672]
[DEBUG] channel:70 2013-08-01 20:07:40,263: using channel_id: 1
[DEBUG] channel:484 2013-08-01 20:07:40,264: Channel open
[DEBUG] comm:35 2013-08-01 20:07:40,266: Successfully established AMQP 
connection
[DEBUG] master:510 2013-08-01 20:07:40,266: Trying to discover any worker 
instances associated with this cluster...
[DEBUG] ec2:246 2013-08-01 20:07:40,267: Establishing boto EC2 connection
[DEBUG] ec2:103 2013-08-01 20:07:40,267: Gathering instance zone, attempt 0
[DEBUG] ec2:108 2013-08-01 20:07:40,270: Instance zone is 'us-east-1d'
[DEBUG] ec2:263 2013-08-01 20:07:40,516: Got boto EC2 connection for region 
'us-east-1'
[DEBUG] ec2:66 2013-08-01 20:07:40,574: Gathering instance id, attempt 0
[DEBUG] ec2:71 2013-08-01 20:07:40,575: Instance ID is 'i-7b386714'
[DEBUG] ec2:295 2013-08-01 20:07:40,639: Adding tag 
'clusterName:gal_oldami_form2' to resource 'i-7b386714'
[DEBUG] ec2:295 2013-08-01 20:07:41,066: Adding tag 'role:master' to resource 
'i-7b386714'
[DEBUG] master:174 2013-08-01 20:07:41,223: ud at manager start: {'access_key': 
'AKIAIUSCRANAJESP3GFQ', 'cloudman_home': '/mnt/cm', 'cluster_name': 
'gal_oldami_form2', 'bucket_default': 'gxy-workshop', 'boot_script_name': 
'cm_boot.py', 'bucket_cluster': 'cm-35f4d40b627583b6949bc5de11bcfecc', 
'boot_script_path': '/tmp/cm', 'role': 'master', 'secret_key': 
'EV12T4PMGSbM1IZmS7ZUJVi9nCvMncnrxXvytacJ', 'password': 'google'}
[DEBUG] pss:25 2013-08-01 20:07:41,224: Configured PSS as master
[DEBUG] master:204 2013-08-01 20:07:41,225: Cheking for and adding any 
preconfigured services
[DEBUG] master:529 2013-08-01 20:07:41,225: Trying to discover any volumes 
attached to this instance...
[DEBUG] base:55 2013-08-01 20:07:41,236: Enabling 'root' controller, class: CM
[DEBUG] buildapp:80 2013-08-01 20:07:41,239: Enabling 'httpexceptions' 
middleware
[DEBUG] buildapp:86 2013-08-01 20:07:41,469: Enabling 'recursive' middleware
[DEBUG] buildapp:106 2013-08-01 20:07:41,719: Enabling 'print debug' middleware
[DEBUG] buildapp:120 2013-08-01 20:07:41,734: Enabling 'error' middleware
[DEBUG] buildapp:130 2013-08-01 20:07:41,735: Enabling 'config' middleware
[DEBUG] buildapp:134 2013-08-01 20:07:41,736: Enabling 'x-forwarded-host' 
middle

Re: [galaxy-dev] job runner upload file

[Nate Coraor]

On Aug 7, 2013, at 7:46 AM, Jasper Jan Koehorst wrote:

> Hello,
> 
> I have a very simple jobrunner script that allows only 1 job to be run as  
> this galaxy is used for one thing in particular which consumes almost all 
> resources.
> 
> To do this I set the following:
> 
> 
>  load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
> 
> 
> This works, but is it possible to create a second worker that is only allowed 
> to be used for uploading files? So people can upload their data already and 
> only enter the queue for the big analysis? Otherwise if they turn their 
> computer off in the evening the upload is gone...

Hi Jasper,

Even if an upload job can't run because it's waiting for a free worker, that 
should not cause the upload to fail as long as the browser finishes 
transferring the file.  Once the file is transferred, the upload job will 
simply wait in the queue until the worker slot is available.

Regardless, you should be able to load the local plugin twice, and utilize 
tool-to-destination mapping and concurrency limits to do what you want, e.g.:













1
1


The extra workers on the upload plugin would allow multiple users' uploads to 
be processed at once.

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Re: [galaxy-dev] ActionInputError undefined

[Nate Coraor]

On Jul 30, 2013, at 5:39 PM, Jim Johnson wrote:

> I was using the quotas api to update a quota amount and got the error:
> 
> galaxy.web.framework ERROR 2013-07-30 15:40:59,149 Uncaught exception in 
> exposed API method:
> Traceback (most recent call last):
>  File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 189, in 
> decorator
>rval = func( self, trans, *args, **kwargs)
>  File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 221, in 
> decorator
>return func( self, trans, *args, **kwargs )
>  File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/quotas.py", line 108, 
> in update
>except ActionInputError, e:
> NameError: global name 'ActionInputError' is not defined
> 
> Was ActionInputError meant to be a class in lib/galaxy/exceptions/__init__.py 
>  ?
> 
> diff -r 951e853b0bcd lib/galaxy/exceptions/__init__.py
> --- a/lib/galaxy/exceptions/__init__.py Tue Jul 30 12:54:02 2013 -0400
> +++ b/lib/galaxy/exceptions/__init__.py Tue Jul 30 16:38:50 2013 -0500
> @@ -21,6 +21,9 @@
> class ItemOwnershipException( MessageException ):
> pass
> 
> +class ActionInputError( MessageException ):
> +pass
> +
> class ObjectNotFound( Exception ):
> """ Accessed object was not found """
> pass

Hi JJ,

That was the idea, I guess I only finished half of that idea before committing 
it...  It should be fixed in e7e82003f235.

Thanks,
--nate

> 
> 
> -- 
> James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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[galaxy-dev] (no subject)

[Vipin TS]

Hello dev-team,

I have updated
code repository
 of our production instance  to the recent
galaxy-dist (10216:ebe87051fadf), now the instance page it is not rendering
in a proper way.

The error message I can see from the log file as follows:
--
x.x.x.x - - [08/Aug/2013:15:00:49 -0400] "GET / HTTP/1.1" 200 - "-"
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko)
Chrome/26.0.1410.63 Safari/537.31"
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] "GET /root/tool_menu HTTP/1.1" 404
- "https://galaxy.cbio.mskcc.org/"; "Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31"
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] "GET /history HTTP/1.1" 200 - "
https://galaxy.cbio.mskcc.org/"; "Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31"
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] "GET /history HTTP/1.1" 500 - "
https://galaxy.cbio.mskcc.org/"; "Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31"

Exception happened during processing of request from ('127.0.0.1', 42042)
Traceback (most recent call last):
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line
1068, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__
self.handle()
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line
442, in handle
BaseHTTPRequestHandler.handle(self)
  File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line
437, in handle_one_request
self.wsgi_execute()
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line
287, in wsgi_execute
self.wsgi_start_response)
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py", line 203,
in __call__
return app(environ, start_response)
  File "/codebase/lib/galaxy/web/framework/middleware/request_id.py", line
12, in __call__
return self.app( environ, start_response )
  File "/codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
  File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", line
68, in __call__
return self.application(environ, replacement_start_response)
  File "/codebase/lib/galaxy/web/framework/middleware/error.py", line 159,
in __call__
exc_info)
  File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", line
67, in replacement_start_response
return start_response( status, headers, exc_info )
  File "/codebase/lib/galaxy/web/framework/middleware/error.py", line 149,
in __call__
app_iter = self.application(environ, sr_checker)
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py", line
84, in __call__
return self.application(environ, start_response)
  File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py",
line 633, in __call__
return self.application(environ, start_response)
  File "/codebase/lib/galaxy/web/framework/base.py", line 132, in __call__
return self.handle_request( environ, start_response )
  File "/codebase/lib/galaxy/web/framework/base.py", line 199, in
handle_request
return body( environ, start_response )
  File "/codebase/lib/galaxy/web/framework/__init__.py", line 985, in render
template.render_context( context )
  File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py", line 319, in
render_context
**kwargs)
  File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
  File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 718, in
_exec_template
callable_(context, *args, **kwargs)
  File "/codebase/database/compiled_templates/root/history.mako.py", line
73, in render_body
if bool( [ data for data in history.active_datasets if data.state in
['running', 'queued', '', None ] ] ):
AttributeError: 'Undefined' object has no attribute 'active_datasets'


Could you point me where I have to look to fix this issue.

thanks in advance,
--/Vipin
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Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3

[Nate Coraor]

On Jul 26, 2013, at 3:51 PM, Leon Mei wrote:

> Dear galaxy developers,
> 
> We have tried today to upgrade our proftpd configuration to make uploading 
> for our galaxy users possible again, both for users with "old" as well as 
> "new" style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3 
> and have the following SQL part in our configuration file based on the post 
> of 
> http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html
> 
> SQLEngine   on
> SQLLogFile  /var/log/proftpd-sql.log
> SQLBackend  postgres
> SQLConnectInfo  galaxy@localhost:5840 galaxyftp <[ourpassword]>
> SQLAuthTypesSHA1 SHA256 PBKDF2
> SQLPasswordPBKDF2 SHA256 1000 24 
> SQLPasswordUserSalt   sql:/GetUserSalt 
> SQLAuthenticate users
> SQLDefaultUID   108
> SQLDefaultGID   116
> SQLDefaultHomedir   /opt/cloudman/pkg/proftpd/var
> SQLUserInfo custom:/LookupGalaxyUser
> SQLNamedQuery  LookupGalaxyUser  SELECT "email, (CASE WHEN substring(password 
> from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE 
> password END) AS 
> password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM 
> galaxy_user WHERE email='%U'"
> SQLNamedQuery  GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 
> 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM 
> galaxy_user WHERE email='%U'" 
> 
> We have executed the LookupGalaxyUser and GetUserSalt commands manually, and 
> the results look good. Now, old users can login via ftp, but for a new user, 
> the authentication still fails:
> 
> 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: >>> cmd_check
> 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using 
> SQLAuthType 'sha1'
> 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler 
> reports failure
> 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using 
> SQLAuthType 'pbkdf2'
> 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler 
> reports failure
> 
> What are we missing?
> 
> Thanks!
> 
> Rob and Leon

Hallo Leon and Rob,

Thanks for working on this, when I'd looked a couple months ago I could not 
find an entirely-ProFTPD way to do this.  I think it may have actually come 
about because I asked about it on their IRC channel. ;)

This may work if you change SQLPasswordPBKDF2:

  SQLPasswordPBKDF2 SHA256 1 24

It'd be great if ProFTPD also supported pulling those values dynamically from 
the database, but Galaxy's PBKDF2 code currently has them hardcoded, so they 
will be static anyway.

--nate

> 
> 
> -- 
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center   
> BioAssist NGS Taskforce 
>  - http://ngs.nbic.nl
> Skype: leon_meiMobile: +31 6 41709231
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Re: [galaxy-dev] Galaxy cannot start last [server:handlerxx]

[Nate Coraor]

On Aug 5, 2013, at 6:23 PM, Rodolfo Aramayo wrote:

> Hi,
> 
> I have a 80 core/1TB RAM Dell server.
> In order improve Galaxy performance I modified the universe_wsgi.ini
> file so as to improve the Scaling and Load Balancing
> as follows:
> 
> # Use a threadpool for the web server instead of creating a thread for each
> # request.
> use_threadpool = True
> 
> # Number of threads in the web server thread pool.
> threadpool_workers = 200
> 
> 
> [server:web0]
> use = egg:Paste#http
> port = 8090
> host = 127.0.0.1
> use_threadpool = true
> threadpool_workers = 10

... snip ...

> [server:handler18]
> use = egg:Paste#http
> port = 8318
> host = 127.0.0.1
> use_threadpool = true
> threadpool_workers = 5
> 
> # [server:handler19]
> # use = egg:Paste#http
> # port = 8319
> # host = 127.0.0.1
> # use_threadpool = true
> # threadpool_workers = 5
> 
> # [server:handler20]
> # use = egg:Paste#http
> # port = 8320
> # host = 127.0.0.1
> # use_threadpool = true
> # threadpool_workers = 5
> 
> 
> job_manager = manager
> job_handlers = 
> handler0,handler1,,handler2,handler3,handler4,handler5,handler6,handler7,handler8,handler9,handler10,handler11,handler12,handler13,handler14,handler15,handler16,handler17,handler18

Hi Rodolfo,

The job_manager and job_handlers options go under the [server:main] section, it 
looks like they are probably underneath the last [server:...] section right now.

Please note that all of these features should now be configured via the job 
configuration file (job_conf.xml), and I've just updated the documentation you 
referred to accordingly.

--nate

> 
> 
> 
> Now the problem I have is that when I start galaxy I cannot get the
> last [server:handler18] to load correclt
> I get the following error:
> 
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,236 Enabling
> 'library_contents' API controller, class: LibraryContentsController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,236 Enabling
> 'group_users' API controller, class: GroupUsersAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,236 Enabling
> 'configuration' API controller, class: ConfigurationController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,237 Enabling
> 'requests' API controller, class: RequestsAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,238 Enabling
> 'folders' API controller, class: FoldersController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,238 Enabling
> 'quotas' API controller, class: QuotaAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,239 Enabling
> 'folder_contents' API controller, class: FolderContentsController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,239 Enabling
> 'roles' API controller, class: RoleAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,240 Enabling
> 'request_types' API controller, class: RequestTypeAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,240 Enabling
> 'users' API controller, class: UserAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,241 Enabling
> 'samples' API controller, class: SamplesAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,241 Enabling
> 'forms' API controller, class: FormDefinitionAPIController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,241 Enabling
> 'permissions' API controller, class: PermissionsController
> galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,242 Enabling
> 'workflows' API controller, class: WorkflowsAPIController
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,242
> app.config.api_folders: False
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,450 Enabling
> 'httpexceptions' middleware
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,450 Enabling
> 'recursive' middleware
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,700 Enabling
> 'error' middleware
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,701 Enabling
> 'trans logger' middleware
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,701 Enabling
> 'x-forwarded-host' middleware
> galaxy.webapps.galaxy.buildapp DEBUG 2013-08-05 17:08:24,701 Enabling
> 'Request ID' middleware
> Starting server in PID 3899.
> Traceback (most recent call last):
>  File "./scripts/paster.py", line 33, in 
>serve.run()
>  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 1049, in run
>invoke(command, command_name, options, args[1:])
>  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 1055, in invoke
>exit_code = runner.run(args)
>  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 220, in run
>result = self.command()
>  File 

Re: [galaxy-dev] qa_url = slyfox?

[Nate Coraor]

On Aug 5, 2013, at 3:14 PM, David Hoover wrote:

> Strangely, I had never noticed this before.  On some tools, there is a link 
> at the top of the tool page that attempts to connect to  
> http://slyfox.bx.psu.edu:8080/, which it can't.  This URL is set via the 
> qa_url directive in the universe_wsgi.ini file.  What is this URL, and what 
> should it be?

Hi David,

This was for BioStar integration that was being under development and testing.  
The work is still in progress, but the link has been removed in recent Galaxy 
releases as it was not ready for stable release.

--nate

> 
> David Hoover
> Helix Systems Staff
> ___
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Re: [galaxy-dev] Upstart script to manage a multi instance load balanced installation

[Nate Coraor]

On Jul 15, 2013, at 6:29 PM, Seth Sims wrote:

> After some work i've created an Upstart script which can manage a load 
> balanced galaxy configuration as described in the wiki. I thought that I 
> would put it on this list for other people to use. The script parses 
> universe_wsgi.ini just like run.sh and spawns all of the servers it finds. It 
> comes in two pieces galaxy.conf and galaxy-worker.conf. Once you place them 
> both in /etc/init and make the proper edits for the environment a server can 
> be started with "sudo start galaxy". The configuration starts the server at 
> boot time and puts all of the instances under the management of upstart which 
> deals with pids, logging to syslog and respawning if an instance crashes.
> I have just gotten this working reasonably well but have done basically no 
> testing so there are bugs to be found. Any comments are welcome if anyone 
> knows a better way to do something here.
> 
> - Seth

Hi Seth,

Thanks for submitting these.  I was about to commit them to the contrib/ 
directory along with the rest of the start scripts, but I was wondering if you 
could avoid running the check/fetch scripts as root by just using `su -c`?

--nate

> 
> *galaxy.conf*
> 
> author "Seth Sims "
> version "0.0.1 test"
> description "galaxy master process. Fetches eggs and spawns all of the 
> servers it finds configured"
> 
> start on started network-services
> 
> # make sure that any eggs we download are at least owned by the galaxy group.
> # we cannot use setuid in this script because only root can issue the "start 
> galaxy-worker" 
> # command. But this way the galaxy instances should still be able to use 
> their eggs.
> setgid galaxy
> 
> # put galaxy root directory here
> chdir /srv/galaxy-dist/
> 
> pre-start script
> date
> echo "checking python version"
> python ./scripts/check_python.py
> [ $? -ne 0 ] && exit 1
> 
> echo "pre-fetching tossing out expired eggs"
> python ./scripts/check_eggs.py -q
> if [ $? -eq 0 ]; then
> echo "Some eggs are out of date, attempting to fetch..."
> python ./scripts/fetch_eggs.py
> if [ $? -eq 0 ]; then
> echo "Fetch Successful."
> else
> echo "Fetch failed."
> fi
> fi
> 
> echo "starting servers"
> SERVERS=`sed -n 's/^\[server:\(.*\)\]/\1/  p' universe_wsgi.ini | xargs 
> echo`
> for SERVER in ${SERVERS} ; do
> echo "starting server ${SERVER}"
> start galaxy-worker SERVER_NAME=${SERVER}
> done
> end script
> 
> post-stop script
> SERVERS=`sed -n 's/^\[server:\(.*\)\]/\1/  p' universe_wsgi.ini | xargs 
> echo`
> date
> echo "stopping galaxy servers".
> for SERVER in ${SERVERS} ; do
> echo "stopping ${SERVER}"
> stop galaxy-worker SERVER_NAME=${SERVER}
> done
> end script
> ---
> *galaxy-worker*
> author "Seth Sims "
> version "0.0.1 test"
> description "Starts a galaxy server instance. This is run from the 
> galaxy.conf file"
> 
> instance $SERVER_NAME
> 
> #make sure we are running as the galaxy user
> setuid galaxy
> setgid galaxy
> 
> #put the galaxy root directory here
> chdir /srv/galaxy-dist/
> 
> #having multiple instances of galaxy using the same egg directory was causing 
> a race
> #condition that was stopping the instances from starting correctly. So give 
> each instance
> #its own directory under /tmp
> env PYTHON_EGG_CACHE=/tmp/${SERVER_NAME}_egg/
> 
> respawn
> 
> script
> exec python ./scripts/paster.py serve universe_wsgi.ini 
> --server-name=${SERVER_NAME}
> end script
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] August 2013 Galaxy Update Newsletter is out

[Dave Clements]

Hi Samuel,

On Wed, Aug 7, 2013 at 8:04 AM, Samuel Lampa  wrote:

> Thanks for the update, Dave!
>
> Was delighted to see that the videos from all the talks (except lightning
> talks) are up at:
> http://wiki.galaxyproject.org/**Events/GCC2013/Program


And I am personally very impressed with the quality of those videos.

>
> I wanted to ask though, are there specific reasons for not using a service
> like YouTube / Vimeo etc?
>

Yes!  Um, but I can't remember what they are (sadly, this is true).  We'll
talk about this on the next outreach call, and I'll post here what we
decide.

And unlike what I said in the email, the Galaxy community has a new *Proteomics
*mailing 
list
.

Thanks,

Dave C

>
> That would make sharing on Google+ / Twitter / Facebook etc much nicer,
> since you get a preview and an in-page embedded player, (possibly) enabled
> commenting etc, which I think would help "spread the word" about Galaxy
> even more.
>
> Just my 5c, and big thanks for the hard work with putting all this up! (I
> know it is a tremendous lot of work)
>
> Best Regards
> // Samuel
>
>
>
> On 07/31/2013 07:51 PM, Dave Clements wrote:
>
>>
>> Hello all,
>>
>> The August 2013 Galaxy Update is now available <
>> http://wiki.galaxyproject.**org/GalaxyUpdates/2013_08
>> >.
>>
>>  --
> Developer at SNIC-UPPMAX www.uppmax.uu.se
> Developer at Dept of Pharm Biosciences www.farmbio.uu.se
>
>


-- 
http://galaxyproject.org/GCC2013
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
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Re: [galaxy-dev] Help with installation

[Nate Coraor]

On Aug 8, 2013, at 12:50 PM, Adam Brenner wrote:

> The issue here is the last line:
> 
> OperationalError: (OperationalError) disk I/O error u'PRAGMA
> table_info("dataset")' ()
> 
> Do you have any security rules setup on the server, quotes, disk
> issues, etc? You can always run a strace on run.sh for a better
> understanding of whats going on.

Specifically, this appears to be a problem with the SQLite database file, 
galaxy-dist/database/universe.sqlite.

--nate

> 
> --
> 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 Thu, Aug 8, 2013 at 4:12 AM, Jurgens de Bruin  wrote:
>> To all,
>> 
>> I am getting the following error when I run sh run.sh :
>> 
>> galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite>=2 egg
>> successfully loaded for sqlite dialect
>> Traceback (most recent call last):
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
>> line 35, in app_factory
>>app = UniverseApplication( global_conf = global_conf, **kwargs )
>>  File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in
>> __init__
>>create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
>> '__file__', None ), self.config.database_engine_options, app=self )
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
>> line 51, in create_or_verify_database
>>dataset_table = Table( "dataset", meta, autoload=True )
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
>> line 318, in __new__
>>table._init(name, metadata, *args, **kw)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
>> line 381, in _init
>>self._autoload(metadata, autoload_with, include_columns)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
>> line 408, in _autoload
>>self, include_columns, exclude_columns
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 2425, in run_callable
>>return conn.run_callable(callable_, *args, **kwargs)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1968, in run_callable
>>return callable_(self, *args, **kwargs)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
>> line 260, in reflecttable
>>return insp.reflecttable(table, include_columns, exclude_columns)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
>> line 370, in reflecttable
>>for col_d in self.get_columns(table_name, schema, **tblkw):
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
>> line 223, in get_columns
>>**kw)
>>  File "", line 1, in 
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
>> line 47, in cache
>>ret = fn(self, con, *args, **kw)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py",
>> line 713, in get_columns
>>(pragma, qtable)))
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1449, in execute
>>params)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1628, in _execute_text
>>statement, parameters
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1698, in _execute_context
>>context)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1691, in _execute_context
>>context)
>>  File
>> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
>> line 331, in do_execute
>>cursor.execute(statement, parameters)
>> OperationalError: (OperationalError) disk I/O error u'PRAGMA
>> table_info("dataset")' ()
>> 
>> Please any help would be appreciated!!
>> 
>> 
>> --
>> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
>> distinti saluti/siong/duì yú/привет
>> 
>> Jurgens de Bruin
>> 
>> _

Re: [galaxy-dev] Galaxy on cluster with LSF scheduler

[Nate Coraor]

On Aug 8, 2013, at 9:48 AM, Auerbach, Kenneth R. wrote:

> Hello,
> 
> Could anyone tell me if there are detailed instructions anywhere for setting 
> up Galaxy on a Linux cluster using an LSF scheduler?
> 
> Thank you.

Hi,

There aren't any instructions specific to LSF because we simply interface with 
it using the DRMAA runner, like we do for PBS Pro and Grid Engine.  You do need 
to install FedStage DRMAA for LSF since Platform doesn't (didn't?) ship a DRMAA 
library with LSF:

http://sourceforge.net/projects/lsf-drmaa/

>From there, you can follow the instructions in the cluster/job documentation:

http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
http://wiki.galaxyproject.org/Admin/Config/Jobs

General documentation on setting up a "production" Galaxy system can be found 
at:

http://usegalaxy.org/production

--nate

> 
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 
> 
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[galaxy-dev] From workflow to script

[Victoria D Bohler]

Hello,

A naïve question, is it possible obtained from a galaxy-workflow a shell
script?, if yes, how can I do it?

Thank you in advance for your answer,

Victoria
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Re: [galaxy-dev] Help with installation

[Adam Brenner]

The issue here is the last line:

OperationalError: (OperationalError) disk I/O error u'PRAGMA
table_info("dataset")' ()

Do you have any security rules setup on the server, quotes, disk
issues, etc? You can always run a strace on run.sh for a better
understanding of whats going on.

--
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 Thu, Aug 8, 2013 at 4:12 AM, Jurgens de Bruin  wrote:
> To all,
>
> I am getting the following error when I run sh run.sh :
>
> galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite>=2 egg
> successfully loaded for sqlite dialect
> Traceback (most recent call last):
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in
> __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options, app=self )
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 51, in create_or_verify_database
> dataset_table = Table( "dataset", meta, autoload=True )
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
> line 318, in __new__
> table._init(name, metadata, *args, **kw)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
> line 381, in _init
> self._autoload(metadata, autoload_with, include_columns)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
> line 408, in _autoload
> self, include_columns, exclude_columns
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 2425, in run_callable
> return conn.run_callable(callable_, *args, **kwargs)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1968, in run_callable
> return callable_(self, *args, **kwargs)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
> line 260, in reflecttable
> return insp.reflecttable(table, include_columns, exclude_columns)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
> line 370, in reflecttable
> for col_d in self.get_columns(table_name, schema, **tblkw):
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
> line 223, in get_columns
> **kw)
>   File "", line 1, in 
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
> line 47, in cache
> ret = fn(self, con, *args, **kw)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py",
> line 713, in get_columns
> (pragma, qtable)))
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1449, in execute
> params)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1628, in _execute_text
> statement, parameters
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1698, in _execute_context
> context)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1691, in _execute_context
> context)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
> line 331, in do_execute
> cursor.execute(statement, parameters)
> OperationalError: (OperationalError) disk I/O error u'PRAGMA
> table_info("dataset")' ()
>
> Please any help would be appreciated!!
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
>
> ___
> 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 sear

[galaxy-dev] Galaxy with LSF scheduler

[Auerbach, Kenneth R.]

Hello,

Can anyone tell me if there are detailed instructions anywhere for setting up 
Galaxy on a Linux cluster using an LSF scheduler?

Thank you.
Ken.



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[galaxy-dev] Oasesoptimiser Problem: Transcripts.fa not found

[Ricardo Perez]

Dear all,

When I try to run oasesoptimiser 
 
in Galaxy I get the following error:


Traceback (most recent call last):
  File 
"/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py",
 line 120, in 
if __name__ == "__main__": __main__()
  File 
"/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py",
 line 69, in __main__
for line in open(transcript_path):
IOError: [Errno 2] No such file or directory: 'transcripts.fa'

Anyone knows what is the source of this problem?

Thank you for your time,
--Ricardo Perez
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Re: [galaxy-dev] Map with BWA results in correpted SAM file

[Geert Vandeweyer]

to add on this :

we have similar issues (sam-to-bam conversion fails with similar 
errors). it seems to be related to the BWA output getting messed up, 
with (part of) columns missing or duplicated on some lines.


I have not found a systematic pattern in the errors, they seem to happen 
rather random.




On 08/08/2013 05:06 PM, Moritz Juchler wrote:

Dear Galaxy Community,

I have a local instance and installed 0.5.9-r16 BWA and  the toolshed 
wrapper. The mapping is successful. I then use the Filter Sam Tool on 
the sam file from the alignment, but it spits out this error:


*Dataset 26: Filter SAM on data 24*

Tool execution generated the following error message:
Traceback (most recent call last):
   File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148, 
in 
 if __name__ == "__main__": main()

   File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 
137, in main
 flags = int( fields[flag_col] )
ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433'


I have the same workflow online and did the exact same steps on the 
same fastq files.
Is there anything I am missing? Is there any information I can provide 
to answer this question?


Best
Moritz


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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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[galaxy-dev] Help with installation

[Jurgens de Bruin]

To all,

I am getting the following error when I run sh run.sh :

galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite>=2 egg
successfully loaded for sqlite dialect
Traceback (most recent call last):
  File
"/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/app.py", line 52,
in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
  File
"/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 51, in create_or_verify_database
dataset_table = Table( "dataset", meta, autoload=True )
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
line 318, in __new__
table._init(name, metadata, *args, **kw)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
line 381, in _init
self._autoload(metadata, autoload_with, include_columns)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
line 408, in _autoload
self, include_columns, exclude_columns
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2425, in run_callable
return conn.run_callable(callable_, *args, **kwargs)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1968, in run_callable
return callable_(self, *args, **kwargs)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 260, in reflecttable
return insp.reflecttable(table, include_columns, exclude_columns)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
line 370, in reflecttable
for col_d in self.get_columns(table_name, schema, **tblkw):
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
line 223, in get_columns
**kw)
  File "", line 1, in 
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
line 47, in cache
ret = fn(self, con, *args, **kw)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py",
line 713, in get_columns
(pragma, qtable)))
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute
params)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1628, in _execute_text
statement, parameters
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
  File
"/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
OperationalError: (OperationalError) disk I/O error u'PRAGMA
table_info("dataset")' ()

Please any help would be appreciated!!


-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin
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[galaxy-dev] Galaxy on cluster with LSF scheduler

[Auerbach, Kenneth R.]

Hello,

Could anyone tell me if there are detailed instructions anywhere for setting up 
Galaxy on a Linux cluster using an LSF scheduler?

Thank you.



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[galaxy-dev] Map with BWA results in correpted SAM file

[Moritz Juchler]

Dear Galaxy Community,

I have a local instance and installed 0.5.9-r16 BWA and  the toolshed
wrapper. The mapping is successful. I then use the Filter Sam Tool on the
sam file from the alignment, but it spits out this error:

*Dataset 26: Filter SAM on data 24*
Tool execution generated the following error message:

Traceback (most recent call last):
  File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 148, in 
if __name__ == "__main__": main()
  File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 137, in main
flags = int( fields[flag_col] )
ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433'

I have the same workflow online and did the exact same steps on the same
fastq files.
Is there anything I am missing? Is there any information I can provide to
answer this question?

Best
Moritz
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Re: [galaxy-dev] Help with cluster setup

[Nate Coraor]

On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:

> Yes,and I also have the same confuse about that.Actually when I set 
> server: in the universe_wsgi.ini as follows for a try,my Galaxy doesn't 
> work with Cluster,if I remove server:,it work .

Hi Shenwiyn,

Are you starting all of the servers that you have defined in universe_wsgi.ini? 
 If using run.sh, setting GALAXY_RUN_ALL in the environment will do this for 
you:

http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling

> [server:node01]
> use = egg:Paste#http
> port = 8080
> host = 0.0.0.0
> use_threadpool = true
> threadpool_workers = 5
> This is my job_conf.xml :
> 
> 
> 
>  load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>  load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
> 
> 
> 
> 
> 
> 
> 
> 
>  id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G
>  id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py
>  id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py
>  id="galaxy_external_chown_script">scripts/external_chown_script.py
> 
>
> 

The galaxy_external_* options are only supported with the drmaa plugin, and 
actually only belong in the univese_wsgi.ini for the moment, they have not been 
migrated to the new-style job configuration.  They should also only be used if 
you are attempting to set up "run jobs as the real user" job running 
capabilities.

> Further more when I want to kill my jobs  by clicking 
>  in galaxy web,the job keeps on running in my 
> background.I do not know how to fix this.
> Any help on this would be grateful.Thank you very much.

Job deletion in the pbs runner was recently broken, but a fix for this bug will 
be part of the next stable release (on Monday).

--nate

>  
> shenwiyn
>  
> From: Jurgens de Bruin
> Date: 2013-08-07 19:55
> To: galaxy-dev
> Subject: [galaxy-dev] Help with cluster setup
> Hi,
> 
> This is my first Galaxy installation setup so apologies for stupid questions. 
> I am setting up Galaxy on a Cluster running Torque as the resource manager. I 
> am working through the documentation but I am unclear on some things:
> 
> Firstly I am unable to find : start_job_runners within the universe_wsgi.ini 
> and I dont want to just add this anywhere - any help on this would be create. 
> 
> Further more this is my job_conf.xml :
> 
> 
> 
> 
> 
>  load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> 
> 
>Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
> 
> Jurgens de Bruin
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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> 
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Re: [galaxy-dev] Help with cluster setup

[Nate Coraor]

On Aug 7, 2013, at 7:55 AM, Jurgens de Bruin wrote:

> Hi,
> 
> This is my first Galaxy installation setup so apologies for stupid questions. 
> I am setting up Galaxy on a Cluster running Torque as the resource manager. I 
> am working through the documentation but I am unclear on some things:
> 
> Firstly I am unable to find : start_job_runners within the universe_wsgi.ini 
> and I dont want to just add this anywhere - any help on this would be create. 

Hi Jurgens,

This option was removed from universe_wsgi.ini, the job handler definitions are 
done via the job_conf.xml file now.  The following page explains that syntax:

http://wiki.galaxyproject.org/Admin/Config/Jobs

However, the scaling page was still for the old style of configuration, so I 
have just updated it for the new style:

http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling

> Further more this is my job_conf.xml :
> 
> 
> 
> 
> 
>  load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> 
> 
>Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
> 
> Jurgens de Bruin
> ___
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> and other Galaxy lists, please use the interface at:
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[galaxy-dev] how to generate a workflow with customized tool names

[Jun Fan]

Dear all,

 

  I have a tool which contains the function A,B, and C, the output of
the function is the input of another function. I have developed a wrapper
for this tool using conditional tag to allow users select the function they
want. The label of the outputs (datasets) can be defined by label attribute
in the outputs. So far so good. However, when I tried to create a workflow
from history, the three steps (functions) from the tool are labeled with the
same text (the title of the wrapper). My question is how to customize it,
e.g. function_A_tool_name, function_B_tool_name which clearly tell the users
which function is used instead of the need to check the parameter setting. 

 

Best regards!

Dr Jun Fan

Postdoctoral Researcher

School of Biological and Chemical Sciences

Queen Mary University of London

 

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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock  wrote:
>
> Hi Dave,
>
> The good news is it does seem some of the missing test results I
> had on Monday have been resolved. However, there are still
> others showing with no test results: :(
>
> No test results here (I expect some to pass and some to fail):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a

I've been updating the BLAST+ repository - currently it does
show some failures due to missing test, but there seems to be
test information missing here - and also I'm expecting the
installation to fail with BOOST issues:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec

(The other problems from 1 August look OK now)

Thanks,

Peter
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Re: [galaxy-dev] shed tool dependencies

[Bjoern Gruening]

Hi Geert,

> Hi,
> 
> Is there a default notation to specify perl modules (threading modules) 
> in a tool configuration or in a submission to the toolshed?
> 
> I've got some tools to share that make extensive use of these modules, 
> and they are not default in a perl distribution. Hence, I'd like to 
> inform the users that they need to install these modules (or that they 
> get installed by the the toolshed using cpan ?)

I'm not a perl erxpert but I will shortly explain what I try to do with
R packages and how it works with python modules.

For python we can install every package to a separate directory and add
it to PYTHONPATH. Once it is in PYTHONPATH every script can import the
module. Important is that we have control over the version of the python
module (we can fetch an archived tarball or specify the version with
pip).

https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_biopython_1_61/tool_dependencies.xml

In R that is not so easy to do, because R assumes that the User always
want to install the latest version. But in Galaxy we need to install
every version at any time to enable reproducibility. What we did is to
archive the R tarballs in a github repository and download them from
there, install the tarballs manually and add it to R_LIBS. 
Once it is in R_LIBS we can import it in any scripts.

https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_deseq2_1_0_17/tool_dependencies.xml

You can probably do the same in Perl, also it does not seem as easy as
in python. Please have a look here:

http://stackoverflow.com/questions/540640/how-can-i-install-a-cpan-module-into-a-local-directory
http://learn.perl.org/faq/perlfaq8.html#How-do-I-keep-my-own-module-library-directory-

Once you have done that you can add the library to PERL5LIB any you
should be done.

Please also consider to create an orphan tool dependency if the perl
library is common and the chance is high that other developers are also
interested to use that package. The two examples above are orphan tool
dependencies and are used by other packages.

http://wiki.galaxyproject.org/DefiningRepositoryDependencies

Hope that helps a little bit!
Bjoern

> Best,
> 
> Geert
> 
> 


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[galaxy-dev] shed tool dependencies

[Geert Vandeweyer]

Hi,

Is there a default notation to specify perl modules (threading modules) 
in a tool configuration or in a submission to the toolshed?


I've got some tools to share that make extensive use of these modules, 
and they are not default in a perl distribution. Hence, I'd like to 
inform the users that they need to install these modules (or that they 
get installed by the the toolshed using cpan ?)


Best,

Geert


--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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