How to upload local files in Galaxy
Hi Everyone, I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list. The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally. I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions. Thanks a lot in advance! -Mehmet
Mehmet: It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive. I found that confusing at first too. Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: Hi Everyone, I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list. The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally. I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions. Thanks a lot in advance! -Mehmet ___________________________________________________________ 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/ -- Brad Langhorst langhorst@neb.com<mailto:langhorst@neb.com> 978-380-7564
Brad, Thank you for your fast reply! Looks like "library_import_dir" is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI. Thanks! ========================================= Mehmet Belgin, Ph.D. (mehmet.belgin@oit.gatech.edu) Scientific Computing Consultant | OIT - Academic and Research Technologies Georgia Institute of Technology 258 Fourth Street, Rich Building, Room 326 Atlanta, GA 30332-0700 Office: (404) 385-0665 On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally.
I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
___________________________________________________________ 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:
-- Brad Langhorst langhorst@neb.com 978-380-7564
Hi, There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our local production server here at Institut Curie. We add a tool call "local upload file", that takes as entry parameters the name of the dataset, the type of file and the path to the file you want to upload. At the execution, the bash script behind will remove the output dataset created by Galaxy and replaced it by a symbolic link to the file (so you don't duplicate files). Just to warn you, there could be a security failure with this tool, because if it is locally executed, it will be by the Galaxy applicative user that can potentially have more rights on file than the current user. To go through this failure, we execute this tool on our local cluster (with pbs/torque) as the current user (so if the current user try to upload a file that he doesn't owned, the tool will not be able to create the symbolic link and the user will receive an error on the Galaxy interface). Tell me if you're interested in such a tool, and I send you the xml file and bash script associated. Bests, Alban Le 07/06/2012 20:11, Mehmet Belgin a écrit :
Brad,
Thank you for your fast reply! Looks like "library_import_dir" is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI.
Thanks!
========================================= Mehmet Belgin, Ph.D. (mehmet.belgin@oit.gatech.edu <mailto:mehmet.belgin@oit.gatech.edu>) Scientific Computing Consultant | OIT - Academic and Research Technologies Georgia Institute of Technology 258 Fourth Street, Rich Building, Room 326 Atlanta, GA 30332-0700 Office: (404) 385-0665
On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally.
I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
___________________________________________________________ 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:
-- Brad Langhorst langhorst@neb.com <mailto:langhorst@neb.com> 978-380-7564
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
Hello, I am interested in this "local upload file" tool. Can you please send the files to me as well. Thanks. -Raj On 6/8/12 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our local production server here at Institut Curie. We add a tool call "local upload file", that takes as entry parameters the name of the dataset, the type of file and the path to the file you want to upload. At the execution, the bash script behind will remove the output dataset created by Galaxy and replaced it by a symbolic link to the file (so you don't duplicate files). Just to warn you, there could be a security failure with this tool, because if it is locally executed, it will be by the Galaxy applicative user that can potentially have more rights on file than the current user. To go through this failure, we execute this tool on our local cluster (with pbs/torque) as the current user (so if the current user try to upload a file that he doesn't owned, the tool will not be able to create the symbolic link and the user will receive an error on the Galaxy interface).
Tell me if you're interested in such a tool, and I send you the xml file and bash script associated.
Bests,
Alban
Le 07/06/2012 20:11, Mehmet Belgin a écrit :
Brad,
Thank you for your fast reply! Looks like "library_import_dir" is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI.
Thanks!
========================================= Mehmet Belgin, Ph.D. (mehmet.belgin@oit.gatech.edu <mailto:mehmet.belgin@oit.gatech.edu>) Scientific Computing Consultant | OIT - Academic and Research Technologies Georgia Institute of Technology 258 Fourth Street, Rich Building, Room 326 Atlanta, GA 30332-0700 Office: (404) 385-0665
On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally.
I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
___________________________________________________________ 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:
-- Brad Langhorst langhorst@neb.com <mailto:langhorst@neb.com> 978-380-7564
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
-- Bio-informatics consultant GGF (http://dna.uga.edu) and QBCG (http://qbcg.uga.edu) 706-542-6092 (8-12 Tuesday, Thursday and Friday) 706-542-6877 (8-12 Monday, Wednesday and Friday) 706-583-0442 (12-5 All week)
On Fri, Jun 8, 2012 at 2:38 PM, Raj Ayyampalayam <raj76@uga.edu> wrote:
Hello,
I am interested in this "local upload file" tool. Can you please send the files to me as well.
Thanks. -Raj
This seems a potentially very useful tool, so putting it on the Galaxy Tool Shed seems like a better idea (with suitable warnings in the documentation). Peter
On Jun 8, 2012, at 8:42 AM, Peter Cock wrote:
On Fri, Jun 8, 2012 at 2:38 PM, Raj Ayyampalayam <raj76@uga.edu> wrote:
Hello,
I am interested in this "local upload file" tool. Can you please send the files to me as well.
Thanks. -Raj
This seems a potentially very useful tool, so putting it on the Galaxy Tool Shed seems like a better idea (with suitable warnings in the documentation).
Peter
I agree with making the tool more widely available. Just to note, though, Nate and I had a discussion on list about this a while back. As Brad mentioned, if you follow the guidelines for FTP import, any method used (not just FTP, but scp, sftp, grid-ftp, etc.) to get data into the 'FTP' import folder works as long as permissions on the data are set so the galaxy user on the cluster end can read the data. We had our local cluster admins set up a link to the user's galaxy import folder in their home directory, so users can basically do this: scp mydata.fastq.gz username@biocluster.igb.illinois.edu:galaxy-upload At the moment this is importing directly to the cluster that galaxy resides on, but we could set this up to import server side. Nate had also indicated the 'FTP-ness' in the documentation and web page would be genericized, but this obviously hasn't happened yet… Aside: are symlinks working with FTP imports? We have a few users who would like the ability to work on the command line and within Galaxy w/o having to copy large files, so having a single data source would be nice. chris
From: Fields, Christopher J [mailto:cjfields@illinois.edu] [SNIP] if you follow the guidelines for FTP import, any method used (not just FTP, but scp, sftp, grid-ftp, etc.) to get data into the 'FTP' import folder works as long as permissions on the data are set so the galaxy user on the cluster end can read the data.
From our investigations, the galaxy user needs to *own* the file, not just be able to read it. The reason is that galaxy does a shutil.move, which calls copy2 to give the new file the same permissions as the old, which calls copystat, which calls os.chmod, which requires galaxy to be the owner.
This seems to be true at least on our old version of Galaxy, though perhaps it's been fixed in the last few months.
We had our local cluster admins set up a link to the user's galaxy import folder in their home directory, so users can basically do this:
scp mydata.fastq.gz username@biocluster.igb.illinois.edu:galaxy-upload
We wanted to do just that, but we kept getting permission errors. In the end, we needed to add a cron job that runs every minute as root and does a chown galaxy on any files appearing in the upload directories. Please let me know if I'm missing something. I'd be happy to turn off the cron. Thanks, -Amir Karger
Hi all, Despite the possible security failure, I push the upload_local_tool in main toolshed under the "data source" repository. I notice about the possible security failure and the way to fix it. I also have a simple 5 minutes method to modify existing tools to allow users to choose the directory where to write the outputs (to keep working with your own tree whitout breaking Galaxy database links). Tell me if you are interested in this method.. Bests, Alban
Hello,
I am interested in this "local upload file" tool. Can you please send the files to me as well.
Thanks. -Raj
On 6/8/12 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our local production server here at Institut Curie. We add a tool call "local upload file", that takes as entry parameters the name of the dataset, the type of file and the path to the file you want to upload. At the execution, the bash script behind will remove the output dataset created by Galaxy and replaced it by a symbolic link to the file (so you don't duplicate files). Just to warn you, there could be a security failure with this tool, because if it is locally executed, it will be by the Galaxy applicative user that can potentially have more rights on file than the current user. To go through this failure, we execute this tool on our local cluster (with pbs/torque) as the current user (so if the current user try to upload a file that he doesn't owned, the tool will not be able to create the symbolic link and the user will receive an error on the Galaxy interface).
Tell me if you're interested in such a tool, and I send you the xml file and bash script associated.
Bests,
Alban
Le 07/06/2012 20:11, Mehmet Belgin a écrit :
Brad,
Thank you for your fast reply! Looks like "library_import_dir" is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI.
Thanks!
========================================= Mehmet Belgin, Ph.D. (mehmet.belgin@oit.gatech.edu <mailto:mehmet.belgin@oit.gatech.edu>) Scientific Computing Consultant | OIT - Academic and Research Technologies Georgia Institute of Technology 258 Fourth Street, Rich Building, Room 326 Atlanta, GA 30332-0700 Office: (404) 385-0665
On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally.
I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
___________________________________________________________ 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:
-- Brad Langhorst langhorst@neb.com <mailto:langhorst@neb.com> 978-380-7564
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
-- Bio-informatics consultant GGF (http://dna.uga.edu) and QBCG (http://qbcg.uga.edu) 706-542-6092 (8-12 Tuesday, Thursday and Friday) 706-542-6877 (8-12 Monday, Wednesday and Friday) 706-583-0442 (12-5 All week)
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
Re, My bad: upload_local_tool -> upload_local_file tool Bests, Alban
Hi all,
Despite the possible security failure, I push the upload_local_tool in main toolshed under the "data source" repository.
I notice about the possible security failure and the way to fix it.
I also have a simple 5 minutes method to modify existing tools to allow users to choose the directory where to write the outputs (to keep working with your own tree whitout breaking Galaxy database links). Tell me if you are interested in this method.. Bests,
Alban
Hello,
I am interested in this "local upload file" tool. Can you please send the files to me as well.
Thanks. -Raj
On 6/8/12 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our local production server here at Institut Curie. We add a tool call "local upload file", that takes as entry parameters the name of the dataset, the type of file and the path to the file you want to upload. At the execution, the bash script behind will remove the output dataset created by Galaxy and replaced it by a symbolic link to the file (so you don't duplicate files). Just to warn you, there could be a security failure with this tool, because if it is locally executed, it will be by the Galaxy applicative user that can potentially have more rights on file than the current user. To go through this failure, we execute this tool on our local cluster (with pbs/torque) as the current user (so if the current user try to upload a file that he doesn't owned, the tool will not be able to create the symbolic link and the user will receive an error on the Galaxy interface).
Tell me if you're interested in such a tool, and I send you the xml file and bash script associated.
Bests,
Alban
Le 07/06/2012 20:11, Mehmet Belgin a écrit :
Brad,
Thank you for your fast reply! Looks like "library_import_dir" is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI.
Thanks!
========================================= Mehmet Belgin, Ph.D. (mehmet.belgin@oit.gatech.edu <mailto:mehmet.belgin@oit.gatech.edu>) Scientific Computing Consultant | OIT - Academic and Research Technologies Georgia Institute of Technology 258 Fourth Street, Rich Building, Room 326 Atlanta, GA 30332-0700 Office: (404) 385-0665
On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally.
I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
___________________________________________________________ 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:
-- Brad Langhorst langhorst@neb.com <mailto:langhorst@neb.com> 978-380-7564
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
-- Bio-informatics consultant GGF (http://dna.uga.edu) and QBCG (http://qbcg.uga.edu) 706-542-6092 (8-12 Tuesday, Thursday and Friday) 706-542-6877 (8-12 Monday, Wednesday and Friday) 706-583-0442 (12-5 All week)
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
Hi Alban, Yes, we would very much interested in this tool, since our current workaround is not a desired one (a python mini http server!). Thank you for sharing it :) -Mehmet On Jun 8, 2012, at 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our local production server here at Institut Curie. We add a tool call "local upload file", that takes as entry parameters the name of the dataset, the type of file and the path to the file you want to upload. At the execution, the bash script behind will remove the output dataset created by Galaxy and replaced it by a symbolic link to the file (so you don't duplicate files). Just to warn you, there could be a security failure with this tool, because if it is locally executed, it will be by the Galaxy applicative user that can potentially have more rights on file than the current user. To go through this failure, we execute this tool on our local cluster (with pbs/torque) as the current user (so if the current user try to upload a file that he doesn't owned, the tool will not be able to create the symbolic link and the user will receive an error on the Galaxy interface).
Tell me if you're interested in such a tool, and I send you the xml file and bash script associated.
Bests,
Alban
Le 07/06/2012 20:11, Mehmet Belgin a écrit :
Brad,
Thank you for your fast reply! Looks like "library_import_dir" is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI.
Thanks!
========================================= Mehmet Belgin, Ph.D. (mehmet.belgin@oit.gatech.edu) Scientific Computing Consultant | OIT - Academic and Research Technologies Georgia Institute of Technology 258 Fourth Street, Rich Building, Room 326 Atlanta, GA 30332-0700 Office: (404) 385-0665
On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally.
I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
___________________________________________________________ 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:
-- Brad Langhorst langhorst@neb.com 978-380-7564
___________________________________________________________ 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:
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___________________________________________________________ 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:
participants (7)
-
Alban Lermine -
Fields, Christopher J -
Karger, Amir -
Langhorst, Brad -
Mehmet Belgin -
Peter Cock -
Raj Ayyampalayam