FTP Problem: Users cannot see their uploads files.
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
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:/LookupGalaxyUser 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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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.vandeweyer2@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 --> ___________________________________________________________ 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/ -- 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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___________________________________________________________ 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/
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.vandeweyer2@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 -->
___________________________________________________________ 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:
--
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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
Ok Geert, Thanks a lot, Best regards Mish Date: Tue, 19 Jun 2012 12:30:27 +0200 From: geert.vandeweyer2@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.vandeweyer2@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 --> ___________________________________________________________ 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/ -- 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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- 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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___________________________________________________________ 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/
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
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
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 <misharl@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
___________________________________________________________ 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/
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.baker@gmail.com To: misharl@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 <misharl@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 ___________________________________________________________ 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/
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 <misharl@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.baker@gmail.com To: misharl@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 <misharl@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
___________________________________________________________ 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/
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.baker@gmail.com To: misharl@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 <misharl@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.baker@gmail.com To: misharl@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 <misharl@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 ___________________________________________________________ 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/
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/
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" selected>Copy files into Galaxy <option value="link_to_files">Link to files without copying into Galaxy %else: <option value="copy_files">Copy files into Galaxy <option value="link_to_files" selected>Link 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" selected>Link 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_files">Link to files without copying into Galaxy <option value="copy_files" selected>Copy files into Galaxy %else: <option value="link_to_files" selected>Link to files without copying into Galaxy <option value="copy_files">Copy files into Galaxy %endif </select> Hope this helps! -John On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon <misharl@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/
___________________________________________________________ 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/
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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: chilton@msi.umn.edu To: misharl@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" selected>Copy files into Galaxy <option value="link_to_files">Link to files without copying into Galaxy %else: <option value="copy_files">Copy files into Galaxy <option value="link_to_files" selected>Link 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" selected>Link 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_files">Link to files without copying into Galaxy <option value="copy_files" selected>Copy files into Galaxy %else: <option value="link_to_files" selected>Link to files without copying into Galaxy <option value="copy_files">Copy files into Galaxy %endif </select>
Hope this helps!
-John
On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon <misharl@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/
___________________________________________________________ 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/
Hi John, It works very fine. Thank you again for your help, very useful :). Have a nice day, Mish From: misharl@hotmail.com To: chilton@msi.umn.edu Date: Mon, 2 Dec 2013 08:51:28 +0000 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: chilton@msi.umn.edu To: misharl@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" selected>Copy files into Galaxy <option value="link_to_files">Link to files without copying into Galaxy %else: <option value="copy_files">Copy files into Galaxy <option value="link_to_files" selected>Link 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" selected>Link 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_files">Link to files without copying into Galaxy <option value="copy_files" selected>Copy files into Galaxy %else: <option value="link_to_files" selected>Link to files without copying into Galaxy <option value="copy_files">Copy files into Galaxy %endif </select>
Hope this helps!
-John
On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon <misharl@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/
___________________________________________________________ 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/
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: chilton@msi.umn.edu To: misharl@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" selected>Copy files into Galaxy <option value="link_to_files">Link to files without copying into Galaxy %else: <option value="copy_files">Copy files into Galaxy <option value="link_to_files" selected>Link 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" selected>Link 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_files">Link to files without copying into Galaxy <option value="copy_files" selected>Copy files into Galaxy %else: <option value="link_to_files" selected>Link to files without copying into Galaxy <option value="copy_files">Copy files into Galaxy %endif </select>
Hope this helps!
-John
On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon <misharl@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/
___________________________________________________________ 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/
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I just tried this out and the symbolic links work for me. Can you verify the path they are taking through the UI: "Shared Data" -> "Data Libraries" -> Pick data library -> Add datasets -> Pick "Upload directory of files" under "Upload Option" -> Then the symbolically linked directory should be available under "Server Directory". Note - slightly counter-intuitively 'None" will still be the top option by default at the top - the other directories should be there though. If the symbolically linked directory is not there - the next thing to check is that a normal directory is available if added to the import directory. If yes, then you should make sure that the Galaxy web processes can read the symbolically linked directory - for instance is it mounting the same file systems that the users are creating these symbolic links with, can it read the directory, etc.... Hope this helps, -John On Fri, Dec 6, 2013 at 4:00 AM, Misharl mon <misharl@hotmail.com> wrote:
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: chilton@msi.umn.edu To: misharl@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" selected>Copy files into Galaxy <option value="link_to_files">Link to files without copying into Galaxy %else: <option value="copy_files">Copy files into Galaxy <option value="link_to_files" selected>Link 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" selected>Link 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_files">Link to files without copying into Galaxy <option value="copy_files" selected>Copy files into Galaxy %else: <option value="link_to_files" selected>Link to files without copying into Galaxy <option value="copy_files">Copy files into Galaxy %endif </select>
Hope this helps!
-John
On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon <misharl@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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___________________________________________________________ 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/
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___________________________________________________________ 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/
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participants (4)
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Dannon Baker -
Geert Vandeweyer -
John Chilton -
Misharl mon