Problem using FTP upload
Hello, I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory. ftp_upload_dir = import/users ftp_upload_site = notnothing if a create a import/users/username with username as my login I still get the message: Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password). According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td3934194... I thought I could do a setup such as I am trying now, but now I am not so sure. Any ideas? Best, Jillian
Jillian, Make sure import/users is the full path. IE: /storage/import/users. If you are using the add-on provided by Jon in: http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.h... make sure you add: ftp_upload_dir_identifier = username to universe_wsgi.ini. Save and restart. We have the same setup on our HPC cluster. Users copy their data to the large storage bricks via scp, rsync, etc... -- 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/ aebrenne@uci.edu On Sun, Apr 21, 2013 at 12:00 AM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hello,
I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory.
ftp_upload_dir = import/users ftp_upload_site = notnothing
if a create a import/users/username with username as my login I still get the message:
Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password).
According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td3934194... I thought I could do a setup such as I am trying now, but now I am not so sure.
Any ideas?
Best, Jillian
___________________________________________________________ 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 Adam, Nope, still getting the 'no files found'. Is there any troubleshooting tips you could give me for file permissions? Best, Jillian ________________________________________ From: Adam Brenner [aebrenne@uci.edu] Sent: Sunday, April 21, 2013 9:42 PM To: Jillian Rowe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using FTP upload Jillian, Make sure import/users is the full path. IE: /storage/import/users. If you are using the add-on provided by Jon in: http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.h... make sure you add: ftp_upload_dir_identifier = username to universe_wsgi.ini. Save and restart. We have the same setup on our HPC cluster. Users copy their data to the large storage bricks via scp, rsync, etc... -- 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/ aebrenne@uci.edu On Sun, Apr 21, 2013 at 12:00 AM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hello,
I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory.
ftp_upload_dir = import/users ftp_upload_site = notnothing
if a create a import/users/username with username as my login I still get the message:
Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password).
According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td3934194... I thought I could do a setup such as I am trying now, but now I am not so sure.
Any ideas?
Best, Jillian
___________________________________________________________ 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/
Um... Lets see Jillian. Can the user who is running the Galaxy process access the folders in question? Whats the chown/chmod on the folders? -- 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/ aebrenne@uci.edu On Mon, Apr 22, 2013 at 11:56 PM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hi Adam,
Nope, still getting the 'no files found'. Is there any troubleshooting tips you could give me for file permissions?
Best, Jillian ________________________________________ From: Adam Brenner [aebrenne@uci.edu] Sent: Sunday, April 21, 2013 9:42 PM To: Jillian Rowe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using FTP upload
Jillian,
Make sure import/users is the full path. IE: /storage/import/users.
If you are using the add-on provided by Jon in: http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.h... make sure you add:
ftp_upload_dir_identifier = username
to universe_wsgi.ini. Save and restart.
We have the same setup on our HPC cluster. Users copy their data to the large storage bricks via scp, rsync, etc...
-- 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/ aebrenne@uci.edu
On Sun, Apr 21, 2013 at 12:00 AM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hello,
I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory.
ftp_upload_dir = import/users ftp_upload_site = notnothing
if a create a import/users/username with username as my login I still get the message:
Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password).
According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td3934194... I thought I could do a setup such as I am trying now, but now I am not so sure.
Any ideas?
Best, Jillian
___________________________________________________________ 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/
Well, I just tried as the root user and it still doesn't see them. I'm sure root has access everywhere. ________________________________________ From: Adam Brenner [aebrenne@uci.edu] Sent: Tuesday, April 23, 2013 10:13 AM To: Jillian Rowe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using FTP upload Um... Lets see Jillian. Can the user who is running the Galaxy process access the folders in question? Whats the chown/chmod on the folders? -- 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/ aebrenne@uci.edu On Mon, Apr 22, 2013 at 11:56 PM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hi Adam,
Nope, still getting the 'no files found'. Is there any troubleshooting tips you could give me for file permissions?
Best, Jillian ________________________________________ From: Adam Brenner [aebrenne@uci.edu] Sent: Sunday, April 21, 2013 9:42 PM To: Jillian Rowe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using FTP upload
Jillian,
Make sure import/users is the full path. IE: /storage/import/users.
If you are using the add-on provided by Jon in: http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.h... make sure you add:
ftp_upload_dir_identifier = username
to universe_wsgi.ini. Save and restart.
We have the same setup on our HPC cluster. Users copy their data to the large storage bricks via scp, rsync, etc...
-- 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/ aebrenne@uci.edu
On Sun, Apr 21, 2013 at 12:00 AM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hello,
I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory.
ftp_upload_dir = import/users ftp_upload_site = notnothing
if a create a import/users/username with username as my login I still get the message:
Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password).
According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td3934194... I thought I could do a setup such as I am trying now, but now I am not so sure.
Any ideas?
Best, Jillian
___________________________________________________________ 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/
Well, I just tried as the root user and it still doesn't see them. I'm sure root has access everywhere. ________________________________________ From: Adam Brenner [aebrenne@uci.edu] Sent: Tuesday, April 23, 2013 10:13 AM To: Jillian Rowe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using FTP upload
Um... Lets see Jillian. Can the user who is running the Galaxy process access the folders in question? Whats the chown/chmod on the folders?
-- 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/ aebrenne@uci.edu
On Mon, Apr 22, 2013 at 11:56 PM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hi Adam,
Nope, still getting the 'no files found'. Is there any troubleshooting tips you could give me for file permissions?
Best, Jillian ________________________________________ From: Adam Brenner [aebrenne@uci.edu] Sent: Sunday, April 21, 2013 9:42 PM To: Jillian Rowe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using FTP upload
Jillian,
Make sure import/users is the full path. IE: /storage/import/users.
If you are using the add-on provided by Jon in:
http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.h...
make sure you add:
ftp_upload_dir_identifier = username
to universe_wsgi.ini. Save and restart.
We have the same setup on our HPC cluster. Users copy their data to the large storage bricks via scp, rsync, etc...
-- 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/ aebrenne@uci.edu
On Sun, Apr 21, 2013 at 12:00 AM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote:
Hello,
I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory.
ftp_upload_dir = import/users ftp_upload_site = notnothing
if a create a import/users/username with username as my login I still get the message:
Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password).
According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td3934194...
This is what I have configured for our cluster: ftp_upload_dir = /som/galaxy/users/ ftp_upload_dir_identifier = username (requires Jon's modification http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.h... ) ftp_upload_site = None ^^ can not be left blank. Any value should work. The folder setup/structure for /som/galaxy/users/ looks like so. /som/galaxy/users/aebrenne /som/galaxy/users/panteater ..... Both aebrenne and panteater are users within Galaxy, they just have the @domain.tld part left out. If the folders contain no files, then nothing will be displayed in Galaxy. It does support nested folders, etc... Hopefully that helps, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu On Tue, Apr 23, 2013 at 1:11 AM, Jillian Rowe <jir2004@qatar-med.cornell.edu> wrote: thought I could do a setup such as I am trying now, but now I am not so sure.
Any ideas?
Best, Jillian
___________________________________________________________ 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/
participants (2)
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Adam Brenner -
Jillian Rowe