[galaxy-dev] Galaxy Library: problem with directories which are symlinks

2013-12-06 Thread Misharl mon




Hi everybody,
Our Galaxy users from my lab can upload directories of files ( 
user_library_import_dir in the universe_wsgi.ini). They can upload their 
files by symlink, but  it doesn't work with directories which are symlinks ( in 
the interface, these directories are not shown).
Is there a way to force Galaxy to see directories which are symlinks ( in the 
user_library_import_dir directory)?

Thanks in advance to all,
Mish







 Date: Thu, 28 Nov 2013 15:06:47 -0600
 Subject: Re: [galaxy-dev] Galaxy code: data libraries
 From: chil...@msi.umn.edu
 To: mish...@hotmail.com
 CC: galaxy-dev@lists.bx.psu.edu
 
 I think the relevant piece of code is in
 templates/webapps/galaxy/ibrary/common/common.mako.
 
 The lines
 select name=link_data_only
 %if not link_data_only or
 link_data_only == 'copy_files':
 option value=copy_files
 selectedCopy files into Galaxy
 option
 value=link_to_filesLink to files without copying into Galaxy
 %else:
 option
 value=copy_filesCopy files into Galaxy
 option value=link_to_files
 selectedLink to files without copying into Galaxy
 %endif
 /select
 
 could probably be modified a few different ways. I have not really
 tried this but if you really do want to eliminate copying all together
 you can probably just replace it with:
 
 select name=link_data_only
   option value=link_to_files
 selectedLink to files without copying into Galaxy
 /select
 
 Alternatively, you could probably modify the default to be linking by
 replacing this with:
 
 select name=link_data_only
 %if link_data_only and
 link_data_only == 'copy_files':
 option
 value=link_to_filesLink to files without copying into Galaxy
 option value=copy_files
 selectedCopy files into Galaxy
 %else:
 option value=link_to_files
 selectedLink to files without copying into Galaxy
 option
 value=copy_filesCopy files into Galaxy
 %endif
/select
 
 Hope this helps!
 
 -John
 
 
 
 On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon mish...@hotmail.com wrote:
  Hi eveybody,
 
  Is there a way in the code of Galaxy, to force the users to use link to
  files without copying in Galaxy by hiding the copy files into Galaxy
  option in the interface, when they add datasets in their library? We want to
  avoid users to click on copy files into Galaxy by mistake.
 
 
  Thanks in advance to all
 
  Mish
 
 
 
 
 
 
 
  Hi everybody,
 
 
  In my lab, after upgrading our Galaxy instance to the latest version, we
  have a problem with displaying tabular files.
 
  Any idea from where the problem can come?
 
  Thanks in advance to all.
 
  Mish
 
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Re: [galaxy-dev] Galaxy code: data libraries

2013-12-05 Thread Misharl mon


Hi John,
It works very fine. Thank you again for your help, very useful :).
Have a nice day,
Mish

From: mish...@hotmail.com
To: chil...@msi.umn.edu
Date: Mon, 2 Dec 2013 08:51:28 +
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy code: data libraries








Hi John,

Thank you very much for your reply! I will try this, and inform you if it works 
correctly.

Thank you again,

Mish


 Date: Thu, 28 Nov 2013 15:06:47 -0600
 Subject: Re: [galaxy-dev] Galaxy code: data libraries
 From: chil...@msi.umn.edu
 To: mish...@hotmail.com
 CC: galaxy-dev@lists.bx.psu.edu
 
 I think the relevant piece of code is in
 templates/webapps/galaxy/ibrary/common/common.mako.
 
 The lines
 select name=link_data_only
 %if not link_data_only or
 link_data_only == 'copy_files':
 option value=copy_files
 selectedCopy files into Galaxy
 option
 value=link_to_filesLink to files without copying into Galaxy
 %else:
 option
 value=copy_filesCopy files into Galaxy
 option value=link_to_files
 selectedLink to files without copying into Galaxy
 %endif
 /select
 
 could probably be modified a few different ways. I have not really
 tried this but if you really do want to eliminate copying all together
 you can probably just replace it with:
 
 select name=link_data_only
   option value=link_to_files
 selectedLink to files without copying into Galaxy
 /select
 
 Alternatively, you could probably modify the default to be linking by
 replacing this with:
 
 select name=link_data_only
 %if link_data_only and
 link_data_only == 'copy_files':
 option
 value=link_to_filesLink to files without copying into Galaxy
 option value=copy_files
 selectedCopy files into Galaxy
 %else:
 option value=link_to_files
 selectedLink to files without copying into Galaxy
 option
 value=copy_filesCopy files into Galaxy
 %endif
/select
 
 Hope this helps!
 
 -John
 
 
 
 On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon mish...@hotmail.com wrote:
  Hi eveybody,
 
  Is there a way in the code of Galaxy, to force the users to use link to
  files without copying in Galaxy by hiding the copy files into Galaxy
  option in the interface, when they add datasets in their library? We want to
  avoid users to click on copy files into Galaxy by mistake.
 
 
  Thanks in advance to all
 
  Mish
 
 
 
 
 
 
 
  Hi everybody,
 
 
  In my lab, after upgrading our Galaxy instance to the latest version, we
  have a problem with displaying tabular files.
 
  Any idea from where the problem can come?
 
  Thanks in advance to all.
 
  Mish
 
  ___
  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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  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 code: data libraries

2013-12-02 Thread Misharl mon




Hi John,

Thank you very much for your reply! I will try this, and inform you if it works 
correctly.

Thank you again,

Mish


 Date: Thu, 28 Nov 2013 15:06:47 -0600
 Subject: Re: [galaxy-dev] Galaxy code: data libraries
 From: chil...@msi.umn.edu
 To: mish...@hotmail.com
 CC: galaxy-dev@lists.bx.psu.edu
 
 I think the relevant piece of code is in
 templates/webapps/galaxy/ibrary/common/common.mako.
 
 The lines
 select name=link_data_only
 %if not link_data_only or
 link_data_only == 'copy_files':
 option value=copy_files
 selectedCopy files into Galaxy
 option
 value=link_to_filesLink to files without copying into Galaxy
 %else:
 option
 value=copy_filesCopy files into Galaxy
 option value=link_to_files
 selectedLink to files without copying into Galaxy
 %endif
 /select
 
 could probably be modified a few different ways. I have not really
 tried this but if you really do want to eliminate copying all together
 you can probably just replace it with:
 
 select name=link_data_only
   option value=link_to_files
 selectedLink to files without copying into Galaxy
 /select
 
 Alternatively, you could probably modify the default to be linking by
 replacing this with:
 
 select name=link_data_only
 %if link_data_only and
 link_data_only == 'copy_files':
 option
 value=link_to_filesLink to files without copying into Galaxy
 option value=copy_files
 selectedCopy files into Galaxy
 %else:
 option value=link_to_files
 selectedLink to files without copying into Galaxy
 option
 value=copy_filesCopy files into Galaxy
 %endif
/select
 
 Hope this helps!
 
 -John
 
 
 
 On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon mish...@hotmail.com wrote:
  Hi eveybody,
 
  Is there a way in the code of Galaxy, to force the users to use link to
  files without copying in Galaxy by hiding the copy files into Galaxy
  option in the interface, when they add datasets in their library? We want to
  avoid users to click on copy files into Galaxy by mistake.
 
 
  Thanks in advance to all
 
  Mish
 
 
 
 
 
 
 
  Hi everybody,
 
 
  In my lab, after upgrading our Galaxy instance to the latest version, we
  have a problem with displaying tabular files.
 
  Any idea from where the problem can come?
 
  Thanks in advance to all.
 
  Mish
 
  ___
  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/
 
 
 
 
  ___ 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
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[galaxy-dev] Galaxy code: data libraries

2013-11-28 Thread Misharl mon
Hi eveybody,

Is there a way in the code of Galaxy, to force the users to use link to files 
without copying in Galaxy by hiding the copy files into Galaxy option in the 
interface, when they add datasets in their library? We want to avoid users to 
click on copy files into Galaxy by mistake.


Thanks in advance to all

Mish


















Hi everybody,


In my lab, after upgrading our Galaxy instance to the latest version, we have a 
problem with displaying tabular files.

Any idea from where the problem can come?

Thanks in advance to all.



Mish
  

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in your mail client.  To manage your subscriptions to this

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  http://galaxyproject.org/search/mailinglists/

  

  

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[galaxy-dev] Problem with tabular files

2013-07-29 Thread Misharl mon








Hi everybody,


In my lab, after upgrading our Galaxy instance to the latest version, we have a 
problem with displaying tabular files.

Any idea from where the problem can come?

Thanks in advance to all.

Mish
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[galaxy-dev] Problem with tabular files

2013-07-29 Thread Misharl mon




Hi Dannon,

Thank you very much for replying. The problem is that we cannot display any 
tabular files in the galaxy result panel. The tabular files are correct. We 
have checked the galaxy log, and didn't see anything.


Thank you,

Mish

Date: Mon, 29 Jul 2013 07:57:28 -0400
Subject: Re: [galaxy-dev] Problem with tabular files
From: dannon.ba...@gmail.com
To: mish...@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu

What is the problem you're observing, and do you see any errors in the galaxy 
log or javascript console?
-Dannon

On Mon, Jul 29, 2013 at 5:51 AM, Misharl mon mish...@hotmail.com wrote:












Hi everybody,


In my lab, after upgrading our Galaxy instance to the latest version, we have a 
problem with displaying tabular files.

Any idea from where the problem can come?

Thanks in advance to all.


Mish
  

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Re: [galaxy-dev] Problem with tabular files

2013-07-29 Thread Misharl mon


When i attempt viewing the tabular file, it doesn't download automatically. it 
displays nothing, a blank panel.

Thanks Dannon 



Date: Mon, 29 Jul 2013 09:55:10 -0400
Subject: Re: [galaxy-dev] Problem with tabular files
From: dannon.ba...@gmail.com
To: mish...@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu

What happens when you attempt view the tabular file?  Does it automatically 
download instead of displaying, for example?

On Mon, Jul 29, 2013 at 9:54 AM, Misharl mon mish...@hotmail.com wrote:








Hi Dannon,

Thank you very much for replying. The problem is that we cannot display any 
tabular files in the galaxy result panel. The tabular files are correct. We 
have checked the galaxy log, and didn't see anything.



Thank you,

Mish

Date: Mon, 29 Jul 2013 07:57:28 -0400
Subject: Re: [galaxy-dev] Problem with tabular files
From: dannon.ba...@gmail.com

To: mish...@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu


What is the problem you're observing, and do you see any errors in the galaxy 
log or javascript console?
-Dannon

On Mon, Jul 29, 2013 at 5:51 AM, Misharl mon mish...@hotmail.com wrote:













Hi everybody,


In my lab, after upgrading our Galaxy instance to the latest version, we have a 
problem with displaying tabular files.

Any idea from where the problem can come?

Thanks in advance to all.



Mish
  

___

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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/



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  http://galaxyproject.org/search/mailinglists/

  

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[galaxy-dev] Select all option in FTP Uploading

2012-07-19 Thread Misharl mon

Hi all,

I was wondering how to upload several files at a time, without clicking on 
every checkbox to upload file with FTP. Like creating an select all option, 
is it possible?


Best regards

Mish
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Re: [galaxy-dev] Configuring Proftpd for galaxy.

2012-06-19 Thread Misharl mon

Ok Geert,

Thanks a lot,

Best regards

Mish




Date: Tue, 19 Jun 2012 12:30:27 +0200
From: geert.vandewey...@ua.ac.be
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Configuring Proftpd for galaxy.


  

  
  
You should also set /home/nate/galaxy_dist/database/ftp/%U to the
path were ftp-uploads will be stored. This is specified in
universe_wsgi.ini as ftp_upload_dir = /path/to/galaxy-ftp



Best regards, 



Geert



On 06/18/2012 09:45 AM, Misharl mon wrote:

  
  
  
Hi,



Thank you very much for your reply. I have tried it and i got
504 and 504. So i must replace in this line:



LookupGalaxyUser SELECT 
email,password,'504','504','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'




Best regards



Mish








  Date: Fri, 15 Jun 2012 15:55:02 +0200

  From: geert.vandewey...@ua.ac.be

  To: galaxy-dev@lists.bx.psu.edu

  Subject: Re: [galaxy-dev] Configuring Proftpd for galaxy.

  

  512 is the unix UID (userid) and GID (groupid) of the user
  running the galaxy daemon. 

  

  This should be adapted to meet your situation. in our case it
  is 1009 and 100 for example. 

  

  Look it up using : 

  

  $ id **the username running galaxy**

  

  best regards

  

  Geert Vandeweyer

  

  

  

  On 06/15/2012 03:35 PM, Misharl mon wrote:
  

 

   Hi everybody,



I'm configuring Proftpd so that it can work with Galaxy
installed in a cluster. I don't understand why for the
UID and GID, it has been chosen the number 512?



# Define a custom query for lookup that returns a passwd-like 
entry.  UID and GID should match your Galaxy user.
SQLUserInfo custom:/LookupGalaxyUser138.102.49.9
SQLNamedQuery   LookupGalaxyUser SELECT 
email,password,'512','512','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'





  Because, when a galaxy user tries to connect via
  filezilla to upload files, the Proftpd server 's logs
  shows:chdir (/work/...): Permission denied . I
  think i have a problem with the UID and GID which
  doesn't match somehow?

  

  Thanks in advance to all.

  

  Mish 
  

-- 




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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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-- 

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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Re: [galaxy-dev] Configuring Proftpd for galaxy.

2012-06-18 Thread Misharl mon

Hi,

Thank you very much for your reply. I have tried it and i got 504 and 504. So i 
must replace in this line:

LookupGalaxyUser SELECT 
email,password,'504','504','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'

Best regards

Mish



Date: Fri, 15 Jun 2012 15:55:02 +0200
From: geert.vandewey...@ua.ac.be
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Configuring Proftpd for galaxy.


  

  
  
512 is the unix UID (userid) and GID (groupid) of the user running
the galaxy daemon. 



This should be adapted to meet your situation. in our case it is
1009 and 100 for example. 



Look it up using : 



$ id **the username running galaxy**



best regards



Geert Vandeweyer







On 06/15/2012 03:35 PM, Misharl mon wrote:

  
  
  



  Hi everybody,

  

  I'm configuring Proftpd so that it can work with Galaxy
  installed in a cluster. I don't understand why for the UID and
  GID, it has been chosen the number 512?

  

  # Define a custom query for lookup that returns a passwd-like entry.  
UID and GID should match your Galaxy user.
SQLUserInfo custom:/LookupGalaxyUser138.102.49.9
SQLNamedQuery   LookupGalaxyUser SELECT 
email,password,'512','512','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'

  

  

Because, when a galaxy user tries to connect via filezilla
to upload files, the Proftpd server 's logs shows:chdir
(/work/...): Permission denied
. I think i have a problem with the UID and GID which
doesn't match somehow?



Thanks in advance to all.



Mish 

  
  --
  

  
  

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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] Configuring Proftpd for galaxy.

2012-06-15 Thread Misharl mon




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[galaxy-dev] FTP Problem: Users cannot see their uploads files.

2012-05-09 Thread Misharl mon

Hi everybody,


I have managed to get proftpd to work, it can connect to the galaxy sql 
database, and users can log to upload files in their directory. But there is a 
problem, when a galaxy user logs in the galaxy web platform,  the user can't 
see his upload files since Galaxy doesn't have the rights to open the 
directory. How can i change the permissions in proftpd so that galaxy can open 
the user directory?


Thanks in advance to all.

Mish  ___
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[galaxy-dev] Problem about configuring Proftpd with Mysql and galaxy

2012-05-04 Thread Misharl mon

Hi everyone,

I have a problem about configuring Proftpd and Mysql with galaxy, i have 
followed the steps from the galaxy wiki about ftp. I have created a database 
'galaxy' and a user mmonsoor which has all the rights on the database. I think 
that the reason is about the proftpd.conf, below is a copy of my proftpd.conf:




# This is a basic ProFTPD configuration file (rename it to 
# 'proftpd.conf' for actual use.  It establishes a single server
# and a single anonymous login.  It assumes that you have a user/group
# nobody and ftp for normal operation and anon.

ServerNameGalaxy Server
ServerTypestandalone
DefaultServeron

# Port 21 is the standard FTP port.
Port21

# Don't use IPv6 support by default.
UseIPv6off

# Umask 022 is a good standard umask to prevent new dirs and files
# from being group and world writable.
Umask077

SyslogFacility  DAEMON
SyslogLevel debug

# To prevent DoS attacks, set the maximum number of child processes
# to 30.  If you need to allow more than 30 concurrent connections
# at once, simply increase this value.  Note that this ONLY works
# in standalone mode, in inetd mode you should use an inetd server
# that allows you to limit maximum number of processes per service
# (such as xinetd).
MaxInstances30

# Set the user and group under which the server will run.
Usernobody
Groupnogroup

PassivePorts3 4

# To cause every FTP user to be jailed (chrooted) into their home
# directory, uncomment this line.
DefaultRoot ~

# Automatically create home directory if it doesn't exist
CreateHome  on dirmode 700


# Allow users to overwrite their files
AllowOverwrite  on

# Allow users to resume interrupted uploads
AllowStoreRestart   on




# Normally, we want files to be overwriteable.
AllowOverwriteon

# Bar use of SITE CHMOD by default
Limit SITE_CHMOD
  DenyAll
/Limit


# Bar use of RETR (download) since this is not a public file drop
Limit RETR
  DenyAll
/Limit


# A basic anonymous configuration, no upload directories.  If you do not
# want anonymous users, simply delete this entire Anonymous section.
Anonymous ~ftp
  Userftp
  Groupftp

  # We want clients to be able to login with anonymous as well as ftp
  UserAliasanonymous ftp

  # Limit the maximum number of anonymous logins
  MaxClients10

  # We want 'welcome.msg' displayed at login, and '.message' displayed
  # in each newly chdired directory.
  DisplayLoginwelcome.msg
  DisplayChdir.message

  # Limit WRITE everywhere in the anonymous chroot
  Limit WRITE
DenyAll
  /Limit
/Anonymous


# Do not authenticate against real (system) users
#AuthPAM off

# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine   on
SQLPasswordEncoding hex

# Set up mod_sql to authenticate against the Galaxy database
SQLEngine  on
SQLBackendsql
SQLConnectInfo  galaxy@localhost mmonsoor MyPassword
SQLAuthTypesSHA1
SQLAuthenticate users

# An empty directory in case chroot fails
SQLDefaultHomedir   /var/opt/local/proftpd

# Define a custom query for lookup that returns a passwd-like entry.  UID and 
GID should match your Galaxy user.
SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery   LookupGalaxyUser SELECT 
email,password,'512','512','/home/mmonsoor/galaxy-dist/database/files/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'





I don't know what is wrong about my proftpd.conf? 


Thanks in advance to all.

Mish
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