Re: [galaxy-dev] Two questions
On 07/23/2013 03:17 PM, Peter Cock wrote: On Tue, Jul 23, 2013 at 2:12 PM, Gromobir wrote: On 07/23/2013 02:51 PM, Peter Cock wrote: On Tue, Jul 23, 2013 at 1:45 PM, Gromobir 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 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? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
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. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On 07/23/2013 03:47 PM, Peter Cock wrote: On Tue, Jul 23, 2013 at 2:40 PM, Gromobir 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 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? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir 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 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 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On Tue, Jul 23, 2013 at 2:40 PM, Gromobir 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 tag bit? Does it do anything strange with piping or redirecting stdout? Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On Tue, Jul 23, 2013 at 2:12 PM, Gromobir wrote: > On 07/23/2013 02:51 PM, Peter Cock wrote: >> >> On Tue, Jul 23, 2013 at 1:45 PM, Gromobir 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 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On 07/23/2013 02:51 PM, Peter Cock wrote: On Tue, Jul 23, 2013 at 1:45 PM, Gromobir 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. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir 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 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Two questions
On Apr 9, 2012, at 3:04 AM, Praveen Raj Somarajan wrote: > Hello, > > Just want to clarify two questions: > > 1) Is there a way to get the absolute path of a dataset directly from the > interface? This is sometimes useful to create a local directory of all > required files (by using symlink) if we know the full path. Hi Raj, I'm not clear on whether you mean programmatically or not. If not, you can see the paths to library datasets from their info page if you're an admin. For history datasets, it's not possible to do from the interface, and you have to use the script galaxy-dist/scripts/helper.py. > 2) How do we create a data library from datasets from multiple saved > histories? I could see "upload dataset from current history" option in "Add > dataset" of DataLibrary, but what is the case if files to be uploaded are > distributed in many histories? Do we can another way to accomplish this? There's not a way to do this, unfortunately, without switching to the history that you wish to import from. --nate > > Best, > > Raj > > > > This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely > for the use of the addressee(s). If you are not the intended recipient, > please notify the sender by e-mail and delete the original message. Further, > you are not to copy, disclose, or distribute this e-mail or its contents to > any other person and any such actions that are unlawful. This e-mail may > contain viruses. Ocimum Biosolutions has taken every reasonable precaution to > minimize this risk, but is not liable for any damage you may sustain as a > result of any virus in this e-mail. You should carry out your own virus > checks before opening the e-mail or attachment. > The information contained in this email and any attachments is confidential > and may be subject to copyright or other intellectual property protection. If > you are not the intended recipient, you are not authorized to use or disclose > this information, and we request that you notify us by reply mail or > telephone and delete the original message from your mail system. > > OCIMUMBIO SOLUTIONS (P) LTD > ___ > 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/ ___ 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/
