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/
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