Hi, Thank You for answers, I am able to learn everyday. I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space. Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself. As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me. Some option like tell Galaxy about extension and properties of file, so that it should not replicate. By command line 'x' is working fine. Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya@gmail.com
Hi Do, the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho. Cheers, Bjoern
Hi, Thank You for answers, I am able to learn everyday.
I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space.
Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself.
As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me.
Some option like tell Galaxy about extension and properties of file, so that it should not replicate.
By command line 'x' is working fine.
Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya@gmail.com
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Hi, Thank You for reply. I am still not clear about this website. https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP There are total 4 main points highlighted in this website. Do I have to follow all 4 points ? I have tried just on second point which is Configuring Galaxy As I just need same folder for galaxy where I can put my content directly. Now after sometime I will all of the points mentioned. Next Question is WHY GALAXY IS NOT ACCEPTING .bai files? .bai is indexed form of .bam files. I tried uploading using admin section upload, which not worked. next normal file upload as .bai file is just 6 MB., but not worked. next I write xml file to incorporate samtools index into galaxy. Program run successfully but output file is 0 KB. in all of my try .bai file is 0 KB. I need to upload because my 'x' program is not accepting normal BAM format hence it needs Indexed BAM. Waiting for positive reply. On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning <bjoern.gruening@gmail.com>wrote:
Hi Do,
the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho.
Cheers, Bjoern
Hi,
Thank You for answers, I am able to learn everyday.
I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space.
Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself.
As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me.
Some option like tell Galaxy about extension and properties of file, so that it should not replicate.
By command line 'x' is working fine.
Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya@gmail.com
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Regards, Chetan
Hello Chetan, Björn sent you a different link yesterday. Please read through it - especially this part: *Upload files from filesystem paths*. https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles M. On Tue, Feb 25, 2014 at 5:37 AM, do kadya <dokadya@gmail.com> wrote:
Hi, Thank You for reply. I am still not clear about this website.
https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP
There are total 4 main points highlighted in this website. Do I have to follow all 4 points ? I have tried just on second point which is Configuring Galaxy
As I just need same folder for galaxy where I can put my content directly. Now after sometime I will all of the points mentioned.
Next Question is WHY GALAXY IS NOT ACCEPTING .bai files? .bai is indexed form of .bam files.
I tried uploading using admin section upload, which not worked. next normal file upload as .bai file is just 6 MB., but not worked. next I write xml file to incorporate samtools index into galaxy. Program run successfully but output file is 0 KB.
in all of my try .bai file is 0 KB.
I need to upload because my 'x' program is not accepting normal BAM format hence it needs Indexed BAM.
Waiting for positive reply.
On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning <bjoern.gruening@gmail.com>wrote:
Hi Do,
the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho.
Cheers, Bjoern
Hi,
Thank You for answers, I am able to learn everyday.
I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space.
Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself.
As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me.
Some option like tell Galaxy about extension and properties of file, so that it should not replicate.
By command line 'x' is working fine.
Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya@gmail.com
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Regards, Chetan
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Hi, Thank you very much for link. I was able to solve the issue (whatever images shown are out dated may be. In my system its dropdown menu insted of checkbox to show "link to files without copy"). So can i do same for result ? Another Question: My 'x' software takes tab delimited list of files, as we all know, Galaxy follows its own file name. My 'x' software unable to look for those file. I have tried to upload all fresh so that my have little more impact but same error. I don't know why its unable to look for that. The folder from where I am uploading got all the files in that. Now when I am running my 'x' tool through galaxy, is it possible that its looking for default location of galaxy instead of ( path / folder) which i am using ? Waiting for positive reply. So in short can I have something like, Galaxy, you dont use your location for uploading, searching and writing results of command. Just use my folder and run my commands in that folder only, so that looking for files will be easy, also i will get to know the result at same place. On Tue, Feb 25, 2014 at 9:01 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Chetan,
Björn sent you a different link yesterday. Please read through it - especially this part: *Upload files from filesystem paths*.
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
M.
On Tue, Feb 25, 2014 at 5:37 AM, do kadya <dokadya@gmail.com> wrote:
Hi, Thank You for reply. I am still not clear about this website.
https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP
There are total 4 main points highlighted in this website. Do I have to follow all 4 points ? I have tried just on second point which is Configuring Galaxy
As I just need same folder for galaxy where I can put my content directly. Now after sometime I will all of the points mentioned.
Next Question is WHY GALAXY IS NOT ACCEPTING .bai files? .bai is indexed form of .bam files.
I tried uploading using admin section upload, which not worked. next normal file upload as .bai file is just 6 MB., but not worked. next I write xml file to incorporate samtools index into galaxy. Program run successfully but output file is 0 KB.
in all of my try .bai file is 0 KB.
I need to upload because my 'x' program is not accepting normal BAM format hence it needs Indexed BAM.
Waiting for positive reply.
On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning <bjoern.gruening@gmail.com
wrote:
Hi Do,
the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho.
Cheers, Bjoern
Hi,
Thank You for answers, I am able to learn everyday.
I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space.
Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself.
As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me.
Some option like tell Galaxy about extension and properties of file, so that it should not replicate.
By command line 'x' is working fine.
Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya@gmail.com
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Regards, Chetan
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Hi,
Hi, Thank you very much for link. I was able to solve the issue (whatever images shown are out dated may be. In my system its dropdown menu insted of checkbox to show "link to files without copy").
Yes, can be but the idea is the same?
So can i do same for result ?
???
Another Question:
My 'x' software takes tab delimited list of files, as we all know, Galaxy follows its own file name. My 'x' software unable to look for those file. I have tried to upload all fresh so that my have little more impact but same error. I don't know why its unable to look for that.
Please have a look at the basic Galaxy Tutorials. For example here: http://vimeo.com/79356949 You will find many more videos. In short you need to change the filetype that is associated with your dataset, probably from txt to tabular.
The folder from where I am uploading got all the files in that. Now when I am running my 'x' tool through galaxy, is it possible that its looking for default location of galaxy instead of ( path / folder) which i am using ?
???
Waiting for positive reply.
So in short can I have something like, Galaxy, you dont use your location for uploading, searching and writing results of command. Just use my folder and run my commands in that folder only, so that looking for files will be easy, also i will get to know the result at same place.
No, unless you are using the Galaxy API. With that you can archive partially what you want. Please read the wiki carefully, most of your questions are covered there. Cheers, Bjoern
On Tue, Feb 25, 2014 at 9:01 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Chetan,
Björn sent you a different link yesterday. Please read through it - especially this part: *Upload files from filesystem paths*.
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
M.
On Tue, Feb 25, 2014 at 5:37 AM, do kadya <dokadya@gmail.com> wrote:
Hi, Thank You for reply. I am still not clear about this website.
https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP
There are total 4 main points highlighted in this website. Do I have to follow all 4 points ? I have tried just on second point which is Configuring Galaxy
As I just need same folder for galaxy where I can put my content directly. Now after sometime I will all of the points mentioned.
Next Question is WHY GALAXY IS NOT ACCEPTING .bai files? .bai is indexed form of .bam files.
I tried uploading using admin section upload, which not worked. next normal file upload as .bai file is just 6 MB., but not worked. next I write xml file to incorporate samtools index into galaxy. Program run successfully but output file is 0 KB.
in all of my try .bai file is 0 KB.
I need to upload because my 'x' program is not accepting normal BAM format hence it needs Indexed BAM.
Waiting for positive reply.
On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning <bjoern.gruening@gmail.com
wrote:
Hi Do,
the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho.
Cheers, Bjoern
Hi,
Thank You for answers, I am able to learn everyday.
I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space.
Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself.
As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me.
Some option like tell Galaxy about extension and properties of file, so that it should not replicate.
By command line 'x' is working fine.
Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya@gmail.com
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Regards, Chetan
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
participants (3)
-
Björn Grüning -
do kadya -
Martin Čech