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] Reg: Issue while adding simple repository dependencies for custom tool
Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki.galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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
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
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/
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] Reg: Issue while adding simple repository dependencies for custom tool
This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki.galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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/ Repositories.tar Description: Unix tar archive ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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/ capsule_with_dependencies_localhost_colon_9009_barcode_parse_new_11_janakiram-t1_c0c45deac27f.tar.gz Description: GNU Zip compressed data capsule_localhost_colon_9009_string_occurrence_janakiram-t1_2a86bc3c363a.tar.gz Description: GNU Zip compressed data ___ 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] restarting multiple web workers
Hi Brad I have a hacky shell script that I use to do rolling restarts of our local server: https://github.com/pjbriggs/galaxy-admin-utils/blob/master/rolling-restart.sh Generally it works okay here but you would have to check how it fits into your local setup. I can't guarantee that it's 100% robust. We have multiple web processes so the service appears to be uninterrupted, although obviously you can get anomalies e.g. when some web processes know about a new tool but others don't. HTH Best wishes, Peter On 01/04/14 19:48, Langhorst, Brad wrote: Hi, I’m using the multiple web server stuff described here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling that seems to address the responsiveness issues i see when many users are active. However, when i add a new tool - it does not alway show up (only for one of the workers maybe?) Right now I’m restarting, but this costs a minute or two of downtime as the server starts up. Has anyone experimented with rolling restarts of web server processes? Alternatively, has anyone found a good way to speed up the startup process? Thanks! Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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/
Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
Hi Janaki, can you try to remove this prior_installation_required completely? Also why do you need a repository dependency, I think that is not needed or? Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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] snpEff and FASTQ Summary Statistics errors
Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list of available genomes that in a next step is shown under the tool SnpEff Databases there you can choose which genome annotation you want to install. To sum it up. 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? Then there is something missing from your reinstallation. The data manager is a dependency of the snpeff package and should be installed as well. Can you check if you need to reinstall the dependency manually unter the snpeff tool in your admin panel? Cheers, Bjoern When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. Hope that will help! Bjoern Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databaseshttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4 - Download a new database * BWA indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by manager * SnpEff Databaseshttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1 - Download a new database * BWA indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by Tool Data Table
Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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:
Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
Hi, Bjoern, Yes the summary looks correct. Greg, I have added tool_dependencies.xml to the same custom tool and installed it successfully in my local galaxy. But If I add repository_dependencies.xml to my custom tool and try to install the tool, then galaxy showing an error message that the dependency xml file is invalid. Thanks, JanakiRam On Thu, Apr 3, 2014 at 5:05 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and
Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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
Hi Nilaksha, You should be able to download a file of any size in your browser from Galaxy. Can you try disabling the developer settings in your universe_wsgi.ini file and see if that helps? Info for doing that is here: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Disable_the_developer_settings Thanks for using Galaxy, Dan On Apr 3, 2014, at 5:12 AM, Nilaksha Neththikumara nilakshafree...@gmail.com wrote: 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.de wrote: 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/ ___ 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] exported Workflows can contain full-path information
Hi, if you export workflows it can happen that your *.ga file contains full-path informations to the chromosome len file. For example try to export the mergeCols1 or the trimmer tool. The field chromInfo will have a full path attached. I don't think that will cause any harm, but it would be nice to omit this information. Trello Card is here: https://trello.com/c/TNUvq8X3 Ciao, Bjoern ___ 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] [galaxy-bugs] Galaxy modules deployment
Hello, it is great you want to share tools with others through Galaxy, thank you! We call added software a 'Galaxy tool'. You can start by reading the tool basics in this page: https://wiki.galaxyproject.org/Admin/Tools and then you can browse through wiki where the vast of information about tool creation is available through tutorials. What you want is to 'wrap' your software for use within Galaxy with an XML file (sometimes called 'tool definition file' or 'wrapper') that will define the interactions of Galaxy and your software and the user interface of the tool page in Galaxy. You develop the tool first on your local Galaxy and then after it is working there you can submit your tool to the Tool Shed (Galaxy's appstore - https://wiki.galaxyproject.org/ToolShed). After your tool is in the Tool Shed it can be installed by any Galaxy worldwide. If you have any questions just ask in the dev-list mailing list (CCed in this conversation). Martin, Galaxy team On Thu, Apr 3, 2014 at 12:36 AM, ut...@bioinfo.sastra.edu wrote: Dear Sir/Mam, As a part of our project work, we have developed some Bioinformatics modules such as finding interactions for protein, displaying the contacts. We are interested in deploying our modules in your Galaxy platform. Is that possible? If so, what is the procedure? Can you guide us? Regards, M. Udayakumar, Dept. of Bioinformatics, SASTRA University, Thanjavur,Tamil Nadu, INDIA. ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hello Janaki and Björn, This problematic behavior is a result of a bug in the repository export process which has been fixed in the following changeset which is currently available in the Galaxy central repo. Thanks very much for reporting this. https://bitbucket.org/galaxy/galaxy-central/commits/773578e65580e3488fadc144739d82f86d9b30f3 Greg Von Kuster On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki. galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on
Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
Thanks Greg, I will verify with new changes. Thanks, JanakiRam On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Janaki and Björn, This problematic behavior is a result of a bug in the repository export process which has been fixed in the following changeset which is currently available in the Galaxy central repo. Thanks very much for reporting this. https://bitbucket.org/galaxy/galaxy-central/commits/773578e65580e3488fadc144739d82f86d9b30f3 Greg Von Kuster On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Hi Luca, Could you send your job_conf.xml please? Also, is there any chance that you modified run.sh to set DRMAA_LIBRARY_PATH there (which would override what you set on the command line)? --nate On Thu, Apr 3, 2014 at 9:17 AM, Luca Toldo lucato...@gmail.com wrote: Dear All, after having discovered the mess in which I was, and the incomplete PBS client installation, I've done the following: *1) PBS Pro* a) removed the incomplete pbs installation that I had b) downloaded the latest version from vendor c) installed it in //usr/pbs d) configured e) tested it -- worked well *2) drma-pbs* a) downloaded version 1.0.17 b) compiled it (./configure --with-pbs=/usr/pbs ) without any problem c) installed it in /usr/local/lib 3) modified DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so 4) sh run.sh --stop 5) sh run.sh --daemon Unfortunately, however when I launch a new job I always get the error message galaxy.jobs DEBUG 2014-04-03 15:13:44,306 (261) Working directory for job is: /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261 galaxy.jobs.handler DEBUG 2014-04-03 15:13:44,321 (261) Dispatching to drmaa runner galaxy.jobs DEBUG 2014-04-03 15:13:44,434 (261) Persisting job destination (destination id: pbs_default) galaxy.jobs.handler INFO 2014-04-03 15:13:44,474 (261) Job dispatched galaxy.tools.deps DEBUG 2014-04-03 15:13:44,659 Building dependency shell command for dependency 'clustalw2' galaxy.tools.deps WARNING 2014-04-03 15:13:44,660 Failed to resolve dependency on 'clustalw2', ignoring galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) submitting file /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) command is: python /opt/ngs/bin/galaxy-dist/tools/rgenetics/rgClustalw.py -i /data/imgt.fasta -o /opt/ngs/bin/galaxy-dist/database/files/000/dataset_340.dat -s ALIGNED -l /opt/ngs/bin/galaxy-dist/database/files/000/dataset_341.dat -t Clustal_run -d DNA -f CLUSTAL; return_code=$?; cd /opt/ngs/bin/galaxy-dist; /opt/ngs/bin/galaxy-dist/set_metadata.sh ./database/files /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261 . /opt/ngs/bin/galaxy-dist/universe_wsgi.ini /opt/ngs/bin/galaxy-dist/database/tmp/tmpq4Rmdl /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy.json /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_347_GsBRYB,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_347_dFD5t0,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_347_k0zCP6,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_347_4LVIFs,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_347_jKfp0r /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_348_Fyy0tJ,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_348_9vWiO3,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_348_HL3EIj,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_348_s1gqxk,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_348_hyQkDF; sh -c exit $return_code galaxy.jobs.runners ERROR 2014-04-03 15:13:45,051 (261) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 150, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If from the commandline I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh then I get 1695145.servername ... What can I do now ? ___ 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:
Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
I should have handled the import in the same commit, but did so in the following changeset. It will eliminate the problematic prior_installation_required=False attribute from the repository tag when a capsule is being imported. changeset: 12944:59bd7349a128 tag: tip user:greg date:Thu Apr 03 10:19:46 2014 -0400 summary: Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to False) to the repository tag when a repository was exported. Greg Von Kuster On Apr 3, 2014, at 9:53 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Thanks Greg, I will verify with new changes. Thanks, JanakiRam On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Janaki and Björn, This problematic behavior is a result of a bug in the repository export process which has been fixed in the following changeset which is currently available in the Galaxy central repo. Thanks very much for reporting this. https://bitbucket.org/galaxy/galaxy-central/commits/773578e65580e3488fadc144739d82f86d9b30f3 Greg Von Kuster On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick reply. Please find the attached .tar file of both the repositories. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: This all seems to be fine, can you send me a tarball with both repositories ... Thanks, Bjoern Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: Hi, Did anyone faced this issue ?. I struck here. Please suggest me. Thanks, JanakiRam On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency.
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value namepath dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list of available genomes that in a next step is shown under the tool SnpEff Databases there you can choose which genome annotation you want to install. To sum it up. 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? Then there is something missing from your reinstallation. The data manager is a dependency of the snpeff package and should be installed as well. Can you check if you need to reinstall the dependency manually unter the snpeff tool in your admin panel? Cheers, Bjoern When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. After SnpEff Databases Execute you still need to pick genome of
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Dear there, I am still stuck there for FASTQ Summary Statistics. Could you give me some clues to fix it? Thanks a lot! Best, Xiaofei From: Wang, Xiaofei Sent: Wednesday, April 02, 2014 11:21 AM To: Daniel Blankenberg Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Oh, yes, here it is: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in module if __name__ == __main__: main() File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 32, in main base_counts = aggregator.get_base_counts_for_column( i ) File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py, line 397, in get_base_counts_for_column return self.nuc_index_base[ column ] IndexError: list index out of range From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, April 02, 2014 11:14 AM To: Wang, Xiaofei Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane? Thanks for using Galaxy, Dan On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei xfw...@ku.edu wrote: Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/
Re: [galaxy-dev] Galaxy unhandled exception checking jobs error
Hi John, Thank you so much for this detailed explanation. Before I saw your email I went ahead and manually made changes in the pbs.py script. I didn't follow your mercurial commands and hope that is not a problem down the road (I guess I could use the hg revert option then).This seemed to have solved the problems I was seeing before. Cheers Ravi On Apr 2, 2014, at 7:47 PM, John Chilton jmchil...@gmail.com wrote: This change is very small and was not committed to the stable branch of galaxy-central so I would just modify the your Galaxy's copy of the pbs runner file directly until the next release: % wget https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0/raw -O /tmp/pbs.patch % hg import --no-commit /tmp/pbs.patch When you go to update Galaxy next it will probably warn you that this file has been modified - at that time you can just run the following command to cleanup your Galaxy instance: % hg revert lib/galaxy/jobs/runners/pbs.py Hope this helps. The Galaxy team is actively discussing alternative ways to distribute fixes between large releases - hopefully I can stop e-mailing out random mercurial commands at some point :). Back to your broader question however, the Galaxy release and update process is such that you really shouldn't lose your configuration as a result of updating Galaxy. Galaxy distributes sample tool_conf.xml, universe_wsgi.ini, etc... files but the actual configuration files themselves are not tracked in the Galaxy central repositories so these files should be unaffected by updates. Deviations from this ideal should be rare and I believe will be spelled out the dev news for releases as they occur. Hope this helps. -John On Wed, Apr 2, 2014 at 12:27 PM, Ravi Alla ravi.a...@berkeley.edu wrote: John, Thanks for this. I am new to managing galaxy, but how do I go about updating my galaxy to reflect these changes? I found directions on https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about pulling changes from the bitbucket repository. Does this preserve my previous galaxy settings? Do I have to back up before I do this? I spent considerable time to get galaxy to work on the cluster and don't want to ruin it. Thank you Ravi On Apr 2, 2014, at 9:58 AM, John Chilton jmchil...@gmail.com wrote: This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html. The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0. Hope this helps. -John On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla ravi.a...@berkeley.edu wrote: Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find. galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 366, in monitor self.check_watched_items() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *' Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks ___ 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] picard wrappers to support the rna-seq metrics and downsample sam tools?
I saw from: http://dev.list.galaxyproject.org/contributing-patches-to-toolshed-repos-td4663497.html that B. Langhorst had submitted a change to the picard wrapper to support the rna-seq metrics - has that patch made it into any of the repo's? I'm not seeing it when I install the picard wrappers. I'd prefer not having to manually apply that patch to get the support for running rna-seq metrics. -Brad Zeitner --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org ___ 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] Stopping Upload jobs
Hi List, I've noticed that the mechanisms for catching job termination signals don't seem to apply to uploading jobs. I was having trouble with *any* jobs being terminated until I pulled Nate's changeset 1298d3f from Galaxy central, but it still doesn't work for uploads. It will remove them from the history, but if I restart Galaxy, they are put back into the history (whether or not there is anything actually happening). If the upload.py script is actively running and I delete the job, the history item comes back up during the next watch cycle. I've been experimenting with staging files as part of a job and I notice that if I set the job state to upload during the staging, the job never gets marked as deleted or deleted_new if I try to remove it from the history with the X button - so the logic I have to stop the upload is never run. Thanks for any insight, Carrie Ganote ___ 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] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei, Can you provide some sample data that is causing the issue for you? Thanks, Dan On Apr 3, 2014, at 11:46 AM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, I am still stuck there for FASTQ Summary Statistics. Could you give me some clues to fix it? Thanks a lot! Best, Xiaofei From: Wang, Xiaofei Sent: Wednesday, April 02, 2014 11:21 AM To: Daniel Blankenberg Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Oh, yes, here it is: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in module if __name__ == __main__: main() File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 32, in main base_counts = aggregator.get_base_counts_for_column( i ) File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py, line 397, in get_base_counts_for_column return self.nuc_index_base[ column ] IndexError: list index out of range From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, April 02, 2014 11:14 AM To: Wang, Xiaofei Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane? Thanks for using Galaxy, Dan On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei xfw...@ku.edu wrote: Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Oh, hooray, I figured it out. what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again: java -jar snpEff.jar download dm5.42 Thank you so much! Best, Xiaofei _ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 10:31 AM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value namepath dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list of available genomes that in a next step is shown under the tool SnpEff Databases there you can choose which genome annotation you want to install. To sum it up. 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? Then there is something missing from your reinstallation. The data manager is a dependency of the snpeff package and should be installed as well. Can you check if you need to reinstall the dependency manually unter the snpeff tool in your admin panel? Cheers, Bjoern When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff
Re: [galaxy-dev] picard wrappers to support the rna-seq metrics and downsample sam tools?
Hi Brad, can you please upvote that card? https://trello.com/c/84df6nON Thanks, Bjoern Am 03.04.2014 21:00, schrieb Brad Zeitner: I saw from: http://dev.list.galaxyproject.org/contributing-patches-to-toolshed-repos-td4663497.html that B. Langhorst had submitted a change to the picard wrapper to support the rna-seq metrics - has that patch made it into any of the repo's? I'm not seeing it when I install the picard wrappers. I'd prefer not having to manually apply that patch to get the support for running rna-seq metrics. -Brad Zeitner --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org ___ 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] version of SAM-to-BAM (CloudMap)
Dear there, When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of heterozygous and homozygous variants to subtract) (imported from uploaded file) on local Galaxy instance, I got this [X] , when I wanted to edit the workflow. Also, I got this The following tools are beinge executed with a different version from what was available when this workflow was last saved because the previous version is no longer available for use on this galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it to update the stored tool version. * toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2: using version '1.1.2' instead of version '1.1.3' indicated in this workflow. * ,when I wanted to run the workflow. I know it is the problem with version of SAM-to-BAM. But, when I searched the Tool sheds Search and browse tool sheds, there is only version 1.1.4 for SAM-to-BAM. When I tried to edit the workflow from Workflow ... Edit, I did not find where could I change the version of SAM-to-BAM. When I clicked on SAM-to-BAM on the Workflow Canvas, it showed the version is 1.1.3 for it. Could you tell me which version do I need exactly, and how to figure out this? Thanks a lot! Best, Xiaofei ___ 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] known name outputs shown in /database/files but not in galaxy windows
I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files: dataset_54.dat (my first declared output that it's empty) dataset_54.dat.gem (the output that throws the tool) dataset_54.dat.log (the other output file that throws the tool) dataset_55.dat (my second declared output that it's empty) So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How can I fix these? Thanks ___ 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] known name outputs shown in /database/files but not in galaxy windows
Hi Angelica, It appears that you are attempting to directly name the output files. Instead, use a variable naming method that permits Galaxy to actually name the files accessed by the database, using output with data tags to link any working files (with from_work_dir) and attach attributes (including metadata such as format). This section and the next is where in the Tool Config wiki you'll most likely want to start a review: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set If you need a new datatype, this is the wiki that explains how to define one: https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Hopefully this helps, Jen Galaxy team On 4/3/14 5:13 AM, ANGELICA GOMEZ ROIG wrote: I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files: dataset_54.dat (my first declared output that it's empty) dataset_54.dat.gem (the output that throws the tool) dataset_54.dat.log (the other output file that throws the tool) dataset_55.dat (my second declared output that it's empty) So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How can I fix these? Thanks ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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] Reg: Issue while adding simple repository dependencies for custom tool
Hi Greg/Bjoern, Thanks for all your help. I checkout the galaxy-central code base(previously I am using galaxy-dist code base) and uploaded my custom tool(with both tool and repository dependency) in to toolshed and also installed custom tool from galaxy. The dependency tool also installed successfully. I have few doubts: - When are you planning to merge these changes into galaxy-dist ? - As mentioned in the galaxy wikihttps://wiki.galaxyproject.org/Admin/GetGalaxy we are using galaxy-dist code base. Can we use galaxy-central ? - What is the difference between galaxy-dist and galaxy-central ? Thanks, JanakiRam On Thu, Apr 3, 2014 at 7:54 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, thanks for fixing it Greg. Would it also be possible to get a more concrete error message in such cases where the repository_dependencies.xml file is somehow broken? Thanks, Bjoern Am 03.04.2014 16:22, schrieb Greg Von Kuster: I should have handled the import in the same commit, but did so in the following changeset. It will eliminate the problematic prior_installation_required=False attribute from the repository tag when a capsule is being imported. changeset: 12944:59bd7349a128 tag: tip user:greg date:Thu Apr 03 10:19:46 2014 -0400 summary: Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to False) to the repository tag when a repository was exported. Greg Von Kuster On Apr 3, 2014, at 9:53 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Thanks Greg, I will verify with new changes. Thanks, JanakiRam On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Janaki and Björn, This problematic behavior is a result of a bug in the repository export process which has been fixed in the following changeset which is currently available in the Galaxy central repo. Thanks very much for reporting this. https://bitbucket.org/galaxy/galaxy-central/commits/ 773578e65580e3488fadc144739d82f86d9b30f3 Greg Von Kuster On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug in populating prior_installation_required in repository_dependencies.xml file. He probably knows if that is supposed to work. Greg, to summarize our findings. It seems that if JanakiRam uploads a repository_dependencies.xml file into a local toolshed the prior_installation_required='False' will be inserted. If he tries to install it, Galaxy complains about a wrong syntax inside the repository_dependecies.xml file. Imho prior_installation_required does not make sense in repository_dependencies.xml or? Is that an bug? JanakiRam can you confirm my summary? Thanks, Bjoern Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: Hi, I am using latest checkout from https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my local galaxy code base). Yes, without repository dependency everything working fine. Thanks, JanakiRam On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, I just tested it in the test-toolshed and for me 'prior_installation_required' is not inserted. Which Galaxy version do you use? Please note, that I'm not sure if that is really causing the trouble you have seen. If you remove the repository dependency everything is working as expected? Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Janaki, can you try to remove this prior_installation_required completely? I didn't added 'prior_installation_required' in the repository_dependencies.xml(as this is optional), it got added when I exported repository files from tool shed. Actual repository_dependencies.xml file has below content. ?xml version=1.0? repositories description=test description repository name=string_occurrence owner=janakiram-t1 / /repositories Also why do you need a repository dependency, I think that is not needed or? This is the first time I working with repository dependencies, so for testing I am trying to add simple repository dependency to my custom tool. Cheers, Bjoern Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: Hi Bjoern, I also exported both the repositories from local toolshed. Please find the attached files. Thanks, JanakiRam On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for quick
