Hi all, I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?
FTP or URL
On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡 caizexi123@yahoo.com.cn wrote:
Hi all,
I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?
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Hi All, Thanks for the tip, but could you specify what directory to ftp them to? I have been wondering about this myself but have not found an answer yet. Also, from my limited testing on a local setup on Mac OS X 10.6, it appears that when you upload a file (170 MB fastq file in my case), it gets placed into a directory within /usr/local/Galaxy/database/files/000/ into a file called, "dataset_1.dat". This file is just a text file of the original fastq file so it might be possible to ftp to there but I am not sure that the database or Galaxy will automatically be able to read this. Can anyone comment on how to ftp files to what directory that Galaxy will be able to add to the History? Thanks in advance, Jim
On Dec 1, 2012, at 8:40 AM, shamsher jagat wrote:
FTP or URL
On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> wrote: Hi all,
I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?
___________________________________________________________ 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:
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There is a tutorial on the home page of Galaxy (uploading data using FTP) that shows you step by step how to go through the uploading process. Hope this helps
Giuseppe Ianiri, Ph.D.
________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of James Meador [jmeador@momentapharma.com] Sent: Saturday, December 01, 2012 10:08 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] The qiuck way to upload large file
Hi All, Thanks for the tip, but could you specify what directory to ftp them to? I have been wondering about this myself but have not found an answer yet. Also, from my limited testing on a local setup on Mac OS X 10.6, it appears that when you upload a file (170 MB fastq file in my case), it gets placed into a directory within /usr/local/Galaxy/database/files/000/ into a file called, "dataset_1.dat". This file is just a text file of the original fastq file so it might be possible to ftp to there but I am not sure that the database or Galaxy will automatically be able to read this. Can anyone comment on how to ftp files to what directory that Galaxy will be able to add to the History? Thanks in advance, Jim
On Dec 1, 2012, at 8:40 AM, shamsher jagat wrote:
FTP or URL
On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> wrote: Hi all,
I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?
___________________________________________________________ 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:
***************************************************************************** This email message and any attachments are confidential and may be privileged. It is intended only for the individual(s) to whom it is addressed and may not be saved, copied, printed, disclosed or otherwise used by anyone else. If you are not the intended recipient, kindly notify the sender and delete this email and any attachments immediately. Momenta Pharmaceuticals, Inc.
___________________________________________________________ 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:
Hi Jim
In addition to the FTP/URL methods I recommend to use "Data Libraries". See: http://wiki.galaxyproject.org/Admin/Data%20Libraries/Libraries
also look at the configurations in universe_wsgi.ini:
library_import_dir user_library_import_dir allow_library_path_paste
which gives you many option to access data out side of the Galaxy database/ folder - without duplicating the data.
Regards, Hans-Rudolf
On 12/02/2012 04:37 PM, Ianiri, Giuseppe wrote:
There is a tutorial on the home page of Galaxy (uploading data using FTP) that shows you step by step how to go through the uploading process. Hope this helps
Giuseppe Ianiri, Ph.D.
From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of James Meador [jmeador@momentapharma.com] Sent: Saturday, December 01, 2012 10:08 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] The qiuck way to upload large file
Hi All, Thanks for the tip, but could you specify what directory to ftp them to? I have been wondering about this myself but have not found an answer yet. Also, from my limited testing on a local setup on Mac OS X 10.6, it appears that when you upload a file (170 MB fastq file in my case), it gets placed into a directory within /usr/local/Galaxy/database/files/000/ into a file called, "dataset_1.dat". This file is just a text file of the original fastq file so it might be possible to ftp to there but I am not sure that the database or Galaxy will automatically be able to read this. Can anyone comment on how to ftp files to what directory that Galaxy will be able to add to the History? Thanks in advance, Jim
On Dec 1, 2012, at 8:40 AM, shamsher jagat wrote:
FTP or URL
On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> wrote: Hi all,
I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?
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:
This email message and any attachments are confidential and may be privileged. It is intended only for the individual(s) to whom it is addressed and may not be saved, copied, printed, disclosed or otherwise used by anyone else. If you are not the intended recipient, kindly notify the sender and delete this email and any attachments immediately. Momenta Pharmaceuticals, Inc.
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:
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:
Thank you, Hans-Rudolf and Giuseppe, The Data Libraries is just what I was hoping for and until I get these working, the ftp mode will be very helpful. Best wishes, Jim
On Dec 3, 2012, at 3:49 AM, Hans-Rudolf Hotz wrote:
Hi Jim
In addition to the FTP/URL methods I recommend to use "Data Libraries". See: http://wiki.galaxyproject.org/Admin/Data%20Libraries/Libraries
also look at the configurations in universe_wsgi.ini:
library_import_dir user_library_import_dir allow_library_path_paste
which gives you many option to access data out side of the Galaxy database/ folder - without duplicating the data.
Regards, Hans-Rudolf
On 12/02/2012 04:37 PM, Ianiri, Giuseppe wrote:
There is a tutorial on the home page of Galaxy (uploading data using FTP) that shows you step by step how to go through the uploading process. Hope this helps
Giuseppe Ianiri, Ph.D.
From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of James Meador [jmeador@momentapharma.com] Sent: Saturday, December 01, 2012 10:08 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] The qiuck way to upload large file
Hi All, Thanks for the tip, but could you specify what directory to ftp them to? I have been wondering about this myself but have not found an answer yet. Also, from my limited testing on a local setup on Mac OS X 10.6, it appears that when you upload a file (170 MB fastq file in my case), it gets placed into a directory within /usr/local/Galaxy/database/files/000/ into a file called, "dataset_1.dat". This file is just a text file of the original fastq file so it might be possible to ftp to there but I am not sure that the database or Galaxy will automatically be able to read this. Can anyone comment on how to ftp files to what directory that Galaxy will be able to add to the History? Thanks in advance, Jim
On Dec 1, 2012, at 8:40 AM, shamsher jagat wrote:
FTP or URL
On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> wrote: Hi all,
I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?
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:
This email message and any attachments are confidential and may be privileged. It is intended only for the individual(s) to whom it is addressed and may not be saved, copied, printed, disclosed or otherwise used by anyone else. If you are not the intended recipient, kindly notify the sender and delete this email and any attachments immediately. Momenta Pharmaceuticals, Inc.
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:
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:
***************************************************************************** This email message and any attachments are confidential and may be privileged. It is intended only for the individual(s) to whom it is addressed and may not be saved, copied, printed, disclosed or otherwise used by anyone else. If you are not the intended recipient, kindly notify the sender and delete this email and any attachments immediately. Momenta Pharmaceuticals, Inc.
galaxy-dev@lists.galaxyproject.org
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Hans-Rudolf Hotz -
Ianiri, Giuseppe -
James Meador -
shamsher jagat -
泽 蔡