Hello list, I have two questions regarding galaxy: 1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there. 2.) Currently I get the message "This dataset is large and only the first megabyte is shown below" every time I try to display a file, which is larger than one megabyte. Is it possible to change this size, such that I won't get this message anymore for larger files? Thank you very much in advance! Cheers, Gromobir
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir <gromobir@arcor.de> wrote:
Hello list, I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there.
The "peek" text shown in the history pane (right hand side) is deliberately short. You can get the full stdout and stderr via the "i" icon (well, up to 32kb or something like that). Peter
On 07/23/2013 02:51 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir <gromobir@arcor.de> wrote:
Hello list, I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there. The "peek" text shown in the history pane (right hand side) is deliberately short. You can get the full stdout and stderr via the "i" icon (well, up to 32kb or something like that).
Peter
Hello Peter, Thanks a lot for your reply. I was talking about the stdout, which can be displayed after clicking on the "i" icon. I went to "i"-icon -> stdout and only the last five lines are displayed there.
On Tue, Jul 23, 2013 at 2:12 PM, Gromobir <gromobir@arcor.de> wrote:
On 07/23/2013 02:51 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir <gromobir@arcor.de> wrote:
Hello list, I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there.
The "peek" text shown in the history pane (right hand side) is deliberately short. You can get the full stdout and stderr via the "i" icon (well, up to 32kb or something like that).
Peter
Hello Peter, Thanks a lot for your reply. I was talking about the stdout, which can be displayed after clicking on the "i" icon. I went to "i"-icon -> stdout and only the last five lines are displayed there.
Hmm. Which tool (or is this happening on all tools)? Perhaps the tool wrapper is limiting this? Peter
On 07/23/2013 03:17 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 2:12 PM, Gromobir <gromobir@arcor.de> wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir <gromobir@arcor.de> wrote:
Hello list, I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there. The "peek" text shown in the history pane (right hand side) is deliberately short. You can get the full stdout and stderr via the "i" icon (well, up to 32kb or something like that).
Peter Hello Peter, Thanks a lot for your reply. I was talking about the stdout, which can be displayed after clicking on the "i" icon. I went to "i"-icon -> stdout and only the last five lines are displayed
On 07/23/2013 02:51 PM, Peter Cock wrote: there. Hmm. Which tool (or is this happening on all tools)? Perhaps the tool wrapper is limiting this?
Peter
I'm currently trying to write my own tool. I implemented it using C++ and the standard output std::cout << ... How could I check if any wrapper may be the problem with this?
On Tue, Jul 23, 2013 at 2:40 PM, Gromobir <gromobir@arcor.de> wrote:
Hello Peter, Thanks a lot for your reply. I was talking about the stdout, which can be displayed after clicking on the "i" icon. I went to "i"-icon -> stdout and only the last five lines are displayed there.
Hmm. Which tool (or is this happening on all tools)? Perhaps the tool wrapper is limiting this?
Peter
I'm currently trying to write my own tool. I implemented it using C++ and the standard output std::cout << ... How could I check if any wrapper may be the problem with this?
You could show us the XML for your wrapper, at least the <command> tag bit? Does it do anything strange with piping or redirecting stdout? Peter
On 07/23/2013 03:47 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 2:40 PM, Gromobir <gromobir@arcor.de> wrote:
Hello Peter, Thanks a lot for your reply. I was talking about the stdout, which can be displayed after clicking on the "i" icon. I went to "i"-icon -> stdout and only the last five lines are displayed there. Hmm. Which tool (or is this happening on all tools)? Perhaps the tool wrapper is limiting this?
Peter
I'm currently trying to write my own tool. I implemented it using C++ and the standard output std::cout << ... How could I check if any wrapper may be the problem with this? You could show us the XML for your wrapper, at least the <command> tag bit? Does it do anything strange with piping or redirecting stdout?
Peter
There was a "tail -n 5" hidden in my xml command. Thank you, Peter, for guiding me in the right direction. Any comments concering my other question?
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir <gromobir@arcor.de> wrote:
Hello list, I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there. 2.) Currently I get the message "This dataset is large and only the first megabyte is shown below" every time I try to display a file, which is larger than one megabyte. Is it possible to change this size, such that I won't get this message anymore for larger files?
Thank you very much in advance!
Cheers, Gromobir
On Tue, Jul 23, 2013 at 3:01 PM, Gromobir <gromobir@arcor.de> wrote:
There was a "tail -n 5" hidden in my xml command. Thank you, Peter, for guiding me in the right direction. Any comments concering my other question?
How data files are shown in the central panel depends on the datatype, so the first thing I would ask is which datatype(s) are you looking to change? Peter
On 07/23/2013 04:05 PM, Peter Cock wrote:
2.) Currently I get the message "This dataset is large and only the first megabyte is shown below" every time I try to display a file, which is larger than one megabyte. Is it possible to change this size, such that I won't get this message anymore for larger files?
How data files are shown in the central panel depends on the datatype, so the first thing I would ask is which datatype(s) are you looking to change? I would like to display xhtml files.
participants (2)
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Gromobir -
Peter Cock