Hi, is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful. Cheers, Jelle
Jelle: CAn you tell us a bit more about the types of edits you are doing? Tx, anton On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
Hi,
is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful.
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
Hi, sometimes after uploading a file I will see an error which is very minor, say a header of a column has a space in it where it shouldn't have one. Or a extra line is added in the top of the file which I don't need. This can also happen after I run a tool and the result I get is ok, but I want to edit the result before it goes to the next tool. For a workflow this is probably not what you want, but for some basic analysis or 'playing around' it can become very handy to have. So it is mostly about very small edits, mostly fixing typing errors or removing one or a few lines. Cheers, Jelle 2010/2/24 Anton Nekrutenko <anton@bx.psu.edu>
Jelle:
CAn you tell us a bit more about the types of edits you are doing?
Tx, anton
On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
Hi,
is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful.
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
I second that suggestion - can be a very useful tool. Daniel ----- Original Message ----- From: Jelle Scholtalbers To: Anton Nekrutenko Cc: galaxy-user@bx.psu.edu Sent: Wednesday, February 24, 2010 11:01 AM Subject: Re: [galaxy-user] Text editor Hi, sometimes after uploading a file I will see an error which is very minor, say a header of a column has a space in it where it shouldn't have one. Or a extra line is added in the top of the file which I don't need. This can also happen after I run a tool and the result I get is ok, but I want to edit the result before it goes to the next tool. For a workflow this is probably not what you want, but for some basic analysis or 'playing around' it can become very handy to have. So it is mostly about very small edits, mostly fixing typing errors or removing one or a few lines. Cheers, Jelle 2010/2/24 Anton Nekrutenko <anton@bx.psu.edu> Jelle: CAn you tell us a bit more about the types of edits you are doing? Tx, anton On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote: Hi, is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful. Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org ------------------------------------------------------------------------------ _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Jelle
sometimes after uploading a file I will see an error which is very minor, say a header of a column has a space in it where it shouldn't have one. Or a extra line is added in the top of the file which I don't need.
Have you tried working with the tools from the "Text Manipulation"? ie. "Remove beginning of a file" alone or in combination with "Concatenate queries tail-to-head" will probably solve most of your cases in just a few steps. Regards, Hans
This can also happen after I run a tool and the result I get is ok, but I want to edit the result before it goes to the next tool. For a workflow this is probably not what you want, but for some basic analysis or 'playing around' it can become very handy to have.
So it is mostly about very small edits, mostly fixing typing errors or removing one or a few lines.
Cheers, Jelle
2010/2/24 Anton Nekrutenko <anton@bx.psu.edu>
Jelle:
CAn you tell us a bit more about the types of edits you are doing?
Tx, anton
On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
Hi,
is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful.
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hans, most cases are indeed solved with the tools already available, removing a line from the top was a bad example :) . However if you have a blast result that you don't want to filter on any particular score, but you want to judge by the alignment and the combination of the different scorings after which you want to filter out several lines which don't have any obvious regularity, then a text editor is the simplest solution. I understand that a texteditor is maybe not the best way for getting a clear history, however the other alternative is to get it out of galaxy and do it on your desktop and place it back in. If there is a tool in galaxy it will all stay in galaxy and just with any other tool, when the file is saved a new file is generated and the original remains. If you then want to see the differences between the files you could do a diff. Cheers, Jelle 2010/2/24 Hotz, Hans-Rudolf <hrh@fmi.ch>
Jelle
sometimes after uploading a file I will see an error which is very minor, say a header of a column has a space in it where it shouldn't have one. Or a extra line is added in the top of the file which I don't need.
Have you tried working with the tools from the "Text Manipulation"?
ie. "Remove beginning of a file" alone or in combination with "Concatenate queries tail-to-head" will probably solve most of your cases in just a few steps.
Regards, Hans
This can also happen after I run a tool and the result I get is ok, but I want to edit the result before it goes to the next tool. For a workflow this is probably not what you want, but for some basic analysis or 'playing around' it can become very handy to have.
So it is mostly about very small edits, mostly fixing typing errors or removing one or a few lines.
Cheers, Jelle
2010/2/24 Anton Nekrutenko <anton@bx.psu.edu>
Jelle:
CAn you tell us a bit more about the types of edits you are doing?
Tx, anton
On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
Hi,
is there a possibility to have a very basic text editor within Galaxy
(or
is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful.
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Jelle: The main issue with this is that is your blast output is 500Mb (which is very common) the browser will have a hard time dealing with it even if there is an editor. Isn't filter tool sufficient to help with irregularities? a. On Feb 25, 2010, at 1:17 AM, Jelle Scholtalbers wrote:
Hans,
most cases are indeed solved with the tools already available, removing a line from the top was a bad example :) . However if you have a blast result that you don't want to filter on any particular score, but you want to judge by the alignment and the combination of the different scorings after which you want to filter out several lines which don't have any obvious regularity, then a text editor is the simplest solution. I understand that a texteditor is maybe not the best way for getting a clear history, however the other alternative is to get it out of galaxy and do it on your desktop and place it back in. If there is a tool in galaxy it will all stay in galaxy and just with any other tool, when the file is saved a new file is generated and the original remains. If you then want to see the differences between the files you could do a diff.
Cheers, Jelle
2010/2/24 Hotz, Hans-Rudolf <hrh@fmi.ch> Jelle
sometimes after uploading a file I will see an error which is very minor, say a header of a column has a space in it where it shouldn't have one. Or a extra line is added in the top of the file which I don't need.
Have you tried working with the tools from the "Text Manipulation"?
ie. "Remove beginning of a file" alone or in combination with "Concatenate queries tail-to-head" will probably solve most of your cases in just a few steps.
Regards, Hans
This can also happen after I run a tool and the result I get is ok, but I want to edit the result before it goes to the next tool. For a workflow this is probably not what you want, but for some basic analysis or 'playing around' it can become very handy to have.
So it is mostly about very small edits, mostly fixing typing errors or removing one or a few lines.
Cheers, Jelle
2010/2/24 Anton Nekrutenko <anton@bx.psu.edu>
Jelle:
CAn you tell us a bit more about the types of edits you are doing?
Tx, anton
On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
Hi,
is there a possibility to have a very basic text editor within
Galaxy (or
is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful.
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
The tools available in Galaxy are mostly sufficient indeed, also a tool I added myself to do a substitute based on regular expressions helps in this. But there are some moments that I just miss an edit function which could save me time as I don't have to go through different tools (or down/uploading) to get the end result. As I already mentioned, I only like to see this for small datasets (sizes uptil the maximum displayed in the "display data" screen) as I know that bigger files are just too hard to handle in the browser. Cheers, Jelle PS. The blast result that I mentioned would also be a small file as I'm not going to manually walkthrough 500mb of blast results, I would ofcourse use a filter for that :) 2010/2/25 Anton Nekrutenko <anton@bx.psu.edu>
Jelle:
The main issue with this is that is your blast output is 500Mb (which is very common) the browser will have a hard time dealing with it even if there is an editor. Isn't filter tool sufficient to help with irregularities?
a.
On Feb 25, 2010, at 1:17 AM, Jelle Scholtalbers wrote:
Hans,
most cases are indeed solved with the tools already available, removing a line from the top was a bad example :) . However if you have a blast result that you don't want to filter on any particular score, but you want to judge by the alignment and the combination of the different scorings after which you want to filter out several lines which don't have any obvious regularity, then a text editor is the simplest solution. I understand that a texteditor is maybe not the best way for getting a clear history, however the other alternative is to get it out of galaxy and do it on your desktop and place it back in. If there is a tool in galaxy it will all stay in galaxy and just with any other tool, when the file is saved a new file is generated and the original remains. If you then want to see the differences between the files you could do a diff.
Cheers, Jelle
2010/2/24 Hotz, Hans-Rudolf <hrh@fmi.ch>
Jelle
sometimes after uploading a file I will see an error which is very minor, say a header of a column has a space in it where it shouldn't have one. Or a extra line is added in the top of the file which I don't need.
Have you tried working with the tools from the "Text Manipulation"?
ie. "Remove beginning of a file" alone or in combination with "Concatenate queries tail-to-head" will probably solve most of your cases in just a few steps.
Regards, Hans
This can also happen after I run a tool and the result I get is ok, but I want to edit the result before it goes to the next tool. For a workflow this is probably not what you want, but for some basic analysis or 'playing around' it can become very handy to have.
So it is mostly about very small edits, mostly fixing typing errors or removing one or a few lines.
Cheers, Jelle
2010/2/24 Anton Nekrutenko <anton@bx.psu.edu>
Jelle:
CAn you tell us a bit more about the types of edits you are doing?
Tx, anton
On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
Hi,
is there a possibility to have a very basic text editor within Galaxy
(or
is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful.
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
participants (4)
-
Anton Nekrutenko -
Daniel Sher -
Hotz, Hans-Rudolf -
Jelle Scholtalbers