Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance
Hi, Thanks a lot for the answer. But I'm afraid that detail panel does not give me the path to the dataset. Have you encountered this problem before? Nilaksha On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Nilaksha Use the ! icon (View details) to get the full path to the data set, and the use 'cp' or 'scp' (if not on the same host) on your terminal. Hope this helps, Hans-Rudolf On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote: Hello all, I'm currently successfully running a pipeline for metagenomic analysis on my locally installed galaxy instance and everything seemed to good by far. But when I'm trying to download my processed blast xml output (I used blast+ wrappers for this) , by clicking the small disk button nothing happens. I tried several options. 1) clicked the 'disk' icon to initiate the downloading 2) right clicked the 'disk' icon and tried to use saved linked as, but a dialog box doesnot appear for saving 3) tried copying the link and used curl on bash terminal, but progress bar is stuck at 0%. I think this is happening because my blast output dataset is much larger (around ~10GB) , but if that's the case, how am I supposed to get the data out of galaxy any way?? Thank a lot in advance. Regards! Nilaksha ___ 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/ ___ 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] Problem downloading large processed datasets : galaxy local instance
No, It's not. Btw do you think this problem is causing due to the capacity of the dataset.? have you experienced this before? Thanking you, Nilaksha On Thu, Apr 3, 2014 at 12:43 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: This might be due to different version of Galaxy. Is the Job Command-Line listed? - Depending on the tool, you might find the path there. Hans-Rudolf :Do you have the will also find the path in the job command On 04/03/2014 09:03 AM, Nilaksha Neththikumara wrote: Hi, Thanks a lot for the answer. But I'm afraid that detail panel does not give me the path to the dataset. Have you encountered this problem before? Nilaksha On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Nilaksha Use the ! icon (View details) to get the full path to the data set, and the use 'cp' or 'scp' (if not on the same host) on your terminal. Hope this helps, Hans-Rudolf On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote: Hello all, I'm currently successfully running a pipeline for metagenomic analysis on my locally installed galaxy instance and everything seemed to good by far. But when I'm trying to download my processed blast xml output (I used blast+ wrappers for this) , by clicking the small disk button nothing happens. I tried several options. 1) clicked the 'disk' icon to initiate the downloading 2) right clicked the 'disk' icon and tried to use saved linked as, but a dialog box doesnot appear for saving 3) tried copying the link and used curl on bash terminal, but progress bar is stuck at 0%. I think this is happening because my blast output dataset is much larger (around ~10GB) , but if that's the case, how am I supposed to get the data out of galaxy any way?? Thank a lot in advance. Regards! Nilaksha _ 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/ http://galaxyproject.org/search/mailinglists/ ___ 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] Problem downloading large processed datasets : galaxy local instance
Thanks for the tip. I got admin privileges by creating an admin account, now I can see the full path. So that it basically means, we can't download larger files directly through the browser window but only from tracing the path and copying the file to some other place. Isn't it :) On Thu, Apr 3, 2014 at 2:21 PM, Berner, Thomas thomas.ber...@jki.bund.dewrote: If you can't get admin right maybe your admin will set the following option in your universe.ini on True: # This option allows users to see the full path of datasets via the View # Details option in the history. Administrators can always see this. #expose_dataset_path = False Greetings, Thomas -Ursprüngliche Nachricht- Von: galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] Im Auftrag von Björn Grüning Gesendet: Donnerstag, 3. April 2014 09:13 An: galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance Hi Nilaksha, unfortunately you only see the path if you are an admin. Can you get admin right? Otherwise, maybe downloading via the API would an alternative. Cheers, Bjoern Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara: Hi, Thanks a lot for the answer. But I'm afraid that detail panel does not give me the path to the dataset. Have you encountered this problem before? Nilaksha On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Nilaksha Use the ! icon (View details) to get the full path to the data set, and the use 'cp' or 'scp' (if not on the same host) on your terminal. Hope this helps, Hans-Rudolf On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote: Hello all, I'm currently successfully running a pipeline for metagenomic analysis on my locally installed galaxy instance and everything seemed to good by far. But when I'm trying to download my processed blast xml output (I used blast+ wrappers for this) , by clicking the small disk button nothing happens. I tried several options. 1) clicked the 'disk' icon to initiate the downloading 2) right clicked the 'disk' icon and tried to use saved linked as, but a dialog box doesnot appear for saving 3) tried copying the link and used curl on bash terminal, but progress bar is stuck at 0%. I think this is happening because my blast output dataset is much larger (around ~10GB) , but if that's the case, how am I supposed to get the data out of galaxy any way?? Thank a lot in advance. Regards! Nilaksha ___ 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/ ___ 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/ ___ 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/ ___ 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/
[galaxy-dev] Fetch Taxonomic Representation : Fails : terminated by signal11
I'm running a local instance of Galaxy and have installed all the tool dependencies and generated dependent files for Taxonomy Fetch. After running the tool for like 20 minutes I get the following error. *Dataset 43: Fetch taxonomic representation on data 37* Tool execution generated the following error message: Execution of taxBuilder terminated by signal 11 Any help would be much appreciated. ___ 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/
[galaxy-dev] blast+ wrapper with remote searching
Hello all, The newly developed blast+ wrappers seem to be very useful, but it seems like they do not contain the function to blast against remote servers instead of installing the databases locally. Am I missing something there? I need to do a remote search for a sequence within galaxy instance so I can automate the process. Help is much appreciated. Thanks a lot, Nilaksha ___ 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] blast+ wrapper with remote searching
Thanks a lot for the information. :) I'm new to the field so get confused at times. I started downloading the NCBI databases locally, but I have two questions. 1) There is no proper updating process for the locally installed NCBI databases. (according to my knowledge) So it seems I have to re download the database totally if I need to get them updated. And those databases are almost always being updating. (.sigh) 2) After installing databases, is there a particular way to let galaxy know where are my databases located? So that they can be included in the drop down menu of the blast+ wrappers for me to select :) Thanks a lot in advance Nilaksha Neththikumara. On Wed, Mar 19, 2014 at 3:33 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Mar 19, 2014 at 6:42 AM, Nilaksha Neththikumara nilakshafree...@gmail.com wrote: Hello all, The newly developed blast+ wrappers seem to be very useful, but it seems like they do not contain the function to blast against remote servers instead of installing the databases locally. Am I missing something there? I need to do a remote search for a sequence within galaxy instance so I can automate the process. Help is much appreciated. Thanks a lot, Nilaksha Hi Nilaksha, You are correct, the BLAST+ wrappers for Galaxy don't currently support the -remote option to connect to the NCBI over the internet to run the searches there - we've talked about this though, and I've filed an issue to track this in future: https://github.com/peterjc/galaxy_blast/issues/39 What do you mean by you need remote search for automation? You can download all the NCBI managed databases like NT/NR locally, so most tasks can be done without the -remote option. Peter P.S. The BLAST+ wrappers aren't 'newly developed', work started way back in 2011 ;) ___ 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/
