[galaxy-user] download contains the html file
Hi, I have a tool that works well. However, when I download the results, the results are zipped up but included into the zip file is the *.html file (with the same name as the tool output) do you know how I can stop this from being zipped up? Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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-user] download contains the html file
Sorry I should have provided more detail. After I have executed my tool, I write the html into the dataset_'id'.dat file listing all the output files which I store in extra_files_path (named as dataset_id_files in the database). Thus when I do a download I only want the files stored in dataset_id_files downloaded I don't want/need dataset_'id'.dat, too. Can I stop dataset_id.dat from being included in the zip file? I was thinking I may need to change act_on_multiple_datasets in ~./lib/galaxy/webapps/galaxy/controllers/library_common.py . However, it doesn't seem that this function is called when you click on the download icon on the history panel. Thanks Neil From: Burdett, Neil (CCI, Herston - RBWH) Sent: Friday, 10 January 2014 1:45 PM To: galaxy-user@lists.bx.psu.edu Subject: download contains the html file Hi, I have a tool that works well. However, when I download the results, the results are zipped up but included into the zip file is the *.html file (with the same name as the tool output) do you know how I can stop this from being zipped up? Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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-user] download contains the html file
For those following this thread. I, finally, managed to stop zipping up the html file by commenting out the try block (around line 260) in ~/lib/galaxy/datatypes/data.py Thanks Neil From: Burdett, Neil (CCI, Herston - RBWH) Sent: Friday, 10 January 2014 3:28 PM To: galaxy-user@lists.bx.psu.edu Subject: RE: download contains the html file Sorry I should have provided more detail. After I have executed my tool, I write the html into the dataset_'id'.dat file listing all the output files which I store in extra_files_path (named as dataset_id_files in the database). Thus when I do a download I only want the files stored in dataset_id_files downloaded I don't want/need dataset_'id'.dat, too. Can I stop dataset_id.dat from being included in the zip file? I was thinking I may need to change act_on_multiple_datasets in ~./lib/galaxy/webapps/galaxy/controllers/library_common.py . However, it doesn't seem that this function is called when you click on the download icon on the history panel. Thanks Neil From: Burdett, Neil (CCI, Herston - RBWH) Sent: Friday, 10 January 2014 1:45 PM To: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu Subject: download contains the html file Hi, I have a tool that works well. However, when I download the results, the results are zipped up but included into the zip file is the *.html file (with the same name as the tool output) do you know how I can stop this from being zipped up? Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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-user] Monitoring usage
Hi, I have a local install of Galaxy. Is there something that I could use to monitor the usage on the system, users logged i/using the tools, CPU usage, disk space etc Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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-user] Is anyone using Galaxy with NeuroScience ?
Hi Zeeshan, We're starting to use Galaxy fro neuro-imaging projects particularly detecting the onset on Alzheimer's disease by quantifying the loss of grey matter in the cortex, so we have methods to register and segment brains etc ... Neil From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Zeeshan Ali Shah Sent: Friday, 16 August 2013 8:03 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Is anyone using Galaxy with NeuroScience ? Hi, Is any one using galaxy for Neuroscience and brain imaging ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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-user] History not updating for multiple instances of Galaxy
Hi, I have three instances of galaxy running on the same Linux box. My /etc/apache2/sites-available/default is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-csiro/static/scripts/(.*) /home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-csiro/static/(.*) /home/galaxy/galaxy-csiro/static/$1 [L] RewriteRule ^/galaxy-csiro/favicon.ico /home/galaxy/galaxy-csiro/static/favicon.ico [L] RewriteRule ^/galaxy-csiro/robots.txt /home/galaxy/galaxy-csiro/static/robots.txt [L] RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P] RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R] RewriteRule ^/galaxy-cte/static/style/(.*) /home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-cte/static/scripts/(.*) /home/galaxy/galaxy-cte/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 [L] RewriteRule ^/galaxy-cte/favicon.ico /home/galaxy/galaxy-cte/static/favicon.ico [L] RewriteRule ^/galaxy-cte/robots.txt /home/galaxy/galaxy-cte/static/robots.txt [L] RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P] RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R] RewriteRule ^/galaxy-Newcastle/static/style/(.*) /home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) /home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-Newcastle/static/(.*) /home/galaxy/galaxy-Newcastle/static/$1 [L] RewriteRule ^/galaxy-Newcastle/favicon.ico /home/galaxy/galaxy-Newcastle/static/favicon.ico [L] RewriteRule ^/galaxy-Newcastle/robots.txt /home/galaxy/galaxy-Newcastle/static/robots.txt [L] RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P] I can view all the instances However, when I try and Get Data and upload a file the history side panel remains empty. I can see that the files have been uploaded to (for example) % ls -lrt galaxy-Newcastle/database/files/000/ total 22868 -rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat -rw-rw-r-- 1 galaxy galaxy 187339 Feb 21 13:02 dataset_2.dat -rw-rw-r-- 1 galaxy galaxy 206568 Feb 21 13:03 dataset_3.dat Any ideas much appreciated... The log file state: Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321 127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] GET /galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1 200 - http://barium-rbh/galaxy-Newcastle/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0 galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] POST /galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1 500 - http://barium-rbh/galaxy-Newcastle/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0 Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] GET /galaxy-Newcastle/tool_runner/upload_async_message HTTP/1.1 200 - http://barium-rbh/galaxy-Newcastle/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] GET /galaxy-Newcastle/history HTTP/1.1 200 - http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_message; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0 galaxy.web.framework DEBUG 2013-02-21 13:16:29,261 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - -
[galaxy-user] Workflows
Hi Sorry if these questions are obvious but I just don't know how to find the answers. I'm trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I've got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I've created workflow but don't know how to access this key. Also in the first example it states galaxy_url/api/workflows However I don't have the api/workflows directory structure in my galaxy-dist, do I need to create this? Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Uploading files to history via API
Hi, It seems the API documentation is a bit scarce. I'd like to upload a file from the command line using the API rather than the GUI, but would like to see the file in the history. Does anyone have any information how to do this/ any tools that are available. Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Upload files from filesystem paths
Hi Ross, I don't know of any tools that work in the way I want, but I'm not an expert on tools within Galaxy. Essentially the data in the directories will be fixed. We run a tool from Galaxy that generates some output data, this data then checks the data located under the directories I am trying to upload to Galaxy. There will probably be around 20 directories, and the data produced would then search these directories looking for a closest match once located it would use the remaining files in the directory to complete the process. So for example, the application is segmenting an image, so a part of the image is the output. This is compared with files in the uploaded directories and a file in a particular directory is chosen (as the closest match) then the remaining files in the directory are then used to complete the process. Does that make sense? There would be around 20 files in each directory. Thanks Neil From: Ross [mailto:ross.laza...@gmail.com] Sent: Thursday, 3 January 2013 2:24 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Neil, It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem. On Thu, Jan 3, 2013 at 1:50 PM, neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.commailto:ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto:neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Upload files from filesystem paths
Thanks for the help Ross. Any chance you can point me to the examples you mentioned? Thanks again Neil From: Ross [mailto:ross.laza...@gmail.com] Sent: Friday, 4 January 2013 8:35 AM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Hi, Neal, Thanks - that sounds interesting. Like I said, composite datatypes are designed to manage collections of related files as a unit and this sounds like a potential use case. There are lots of tools and lots of code that can serve as examples but it's definitely not trivial because you will almost certainly be subclassing the Html data class and writing methods to manage those related files (ie extending the guts of Galaxy) and your tools will all need to know how to deal with the managed structure when they get one as an input. You may need to find or build up a programmer with some relevant Galaxy composite datatype experience. There is some documentation but it's not extensive or transparent. Good luck. On Fri, Jan 4, 2013 at 9:19 AM, neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi Ross, I don't know of any tools that work in the way I want, but I'm not an expert on tools within Galaxy. Essentially the data in the directories will be fixed. We run a tool from Galaxy that generates some output data, this data then checks the data located under the directories I am trying to upload to Galaxy. There will probably be around 20 directories, and the data produced would then search these directories looking for a closest match once located it would use the remaining files in the directory to complete the process. So for example, the application is segmenting an image, so a part of the image is the output. This is compared with files in the uploaded directories and a file in a particular directory is chosen (as the closest match) then the remaining files in the directory are then used to complete the process. Does that make sense? There would be around 20 files in each directory. Thanks Neil From: Ross [mailto:ross.laza...@gmail.commailto:ross.laza...@gmail.com] Sent: Thursday, 3 January 2013 2:24 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Neil, It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem. On Thu, Jan 3, 2013 at 1:50 PM, neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.commailto:ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto:neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ The Galaxy User list should be used for the
Re: [galaxy-user] Upload files from filesystem paths
Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Upload files from filesystem paths
Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Using syncing tool in Galaxy
Maybe you should Send this to the galaxy-dev mailing list? galaxy-...@lists.bx.psu.edumailto:galaxy-...@lists.bx.psu.edu Neil From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Sachit Adhikari Sent: Wednesday, 31 October 2012 7:09 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Using syncing tool in Galaxy Hello Everyone, I am about to write a syncing tool for Galaxy like Dropbox using Python with the progress bar. How do I integrate it with galaxy? It would be easy for client to upload files using the syncing tool. Are there any syncing tools available for Galaxy? Thanks ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Batch jobs...
Hi, I've created a workflow that works well. The workflow accepts 2 input files. After uploading all my input files (there is a lot). How can I batch the process, because I don't want to select files manually and run each job manually. Is there a way to batch this action? Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Manage Jobs...
Hi I have a local install of Galaxy running on my desktop. When I'm running a task I expected to see the process under Admin-Manage Jobs but it doesn't appear here. Do I need to set something to see the processes here? Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] No output produced.....
Hi, I have my own image registration tool that I've created on my own local instance of galaxy. The method takes in two images (*.nii.gz) formats and registers them together, and produces one registered *.nii.gz file and a *.trsf matrix file. The first issue encountered was the method was expecting *.nii.gz files as inputs but was receiving *.dat files. I navigated around this problem as shown by the files below: - tool id=RegisterAliBabaAffine name=RegisterAffine descriptiontwo images/description command interpreter=bash$__root_dir__/tools/registration/reg-wrapper.sh $moving $fixed $outputTRSF $outputImage/command - inputs param format=binary name=moving type=data label=Moving Image / param format=binary name=fixed type=data label=Fixed Image / param type=hidden name=outputTRSF value=output.trsf label=trsf file help=Output File must have .trsf extension / param type=hidden name=outputImage value=output.nii.gz label=Image output file help=Output Image File must have .nii.gz extension / /inputs - outputs data format=input name=output_TRSF from_work_dir=output.trsf / data format=input name=output_Image from_work_dir=output.nii.gz / /outputs helpThis tool uses Affine Registration to register two images./help /tool #!/bin/bash MOVING=`mktemp --suffix .nii.gz` FIXED=`mktemp --suffix .nii.gz` cat $1 $MOVING cat $2 $FIXED /usr/local/MILXView.12.08.1/BashScripts/RegisterAliBabaAffine -m $MOVING -f $FIXED -t $3 -o $4 RC=$? if [[ $RC == 0 ]]; then OUTPUTTRSF=`mktemp --suffix .trsf` OUTPUTIMG=`mktemp --suffix .nii.gz` cat $OUTPUTTRSF $3 cat $OUTPUTIMG $4 rm $OUTPUTTRSF rm $OUTPUTIMG fi rm $MOVING rm $FIXED exit $RC This allows them to pass the *.nii.gz files that the registration method is expecting. Everything works fine and I can see output generated in the job_working_dir and the history turns green... galaxy@bmladmin-OptiPlex-745:~$ ls -lrt ~/galaxy-dist/database/job_working_directory/000/27/ total 2940 -rw--- 1 galaxy nogroup 0 Sep 13 10:15 tmpRfHsOP_stderr -rw-r--r-- 1 galaxy nogroup 241 Sep 13 10:35 output.trsf -rw--- 1 galaxy nogroup 80 Sep 13 10:35 tmplmK0V2_stdout -rw-r--r-- 1 galaxy nogroup 2998272 Sep 13 10:38 output.nii.gz However, the problem occurs when the files are copied from ~/galaxy-dist/database/job_working_directory/000/27/ to ~/galaxy-dist/database/files/000/. When this happens the files become size = 0. Any ideas? -rw-r--r-- 1 galaxy nogroup 0 Sep 13 09:36 /home/galaxy/galaxy-dist/database/files/000/dataset_40.dat -rw-r--r-- 1 galaxy nogroup 0 Sep 13 09:36 /home/galaxy/galaxy-dist/database/files/000/dataset_41.dat -rw-r--r-- 1 galaxy nogroup 0 Sep 13 10:38 /home/galaxy/galaxy-dist/database/files/000/dataset_43.dat -rw-r--r-- 1 galaxy nogroup 0 Sep 13 10:38 /home/galaxy/galaxy-dist/database/files/000/dataset_42.dat The output in galaxy.log indicates it is successful: /home/galaxy/galaxy-dist/tools/registration/reg-wrapper.sh /home/galaxy/galaxy-dist/database/files/000/dataset_23.dat /home/galaxy/galaxy-dist/database/files/000/dataset_20.dat output.trsf output.nii.gz galaxy.jobs DEBUG 2012-09-13 10:38:10,334 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-09-13 10:38:10,361 finish(): Moved /home/galaxy/galaxy-dist/database/job_working_directory/000/27/output.trsf to /home/galaxy/galaxy-dist/database/files/000/dataset_42.dat as directed by from_work_dir galaxy.jobs DEBUG 2012-09-13 10:38:10,380 finish(): Moved /home/galaxy/galaxy-dist/database/job_working_directory/000/27/output.nii.gz to /home/galaxy/galaxy-dist/database/files/000/dataset_43.dat as directed by from_work_dir galaxy.jobs DEBUG 2012-09-13 10:38:10,609 job 27 ended Is the issue copying *.nii.gz files and *.trsf file into *.dat files? Anyway around this? I've also modified ~/galaxy-dist/lib/galaxy/jobs/__init__.py (line 363) to change shutil.move To shutil.copy2 (same results) Also put in a different output path to copy to. But essentially we have files with size in ~/galaxy-dist/database/job_working_directory/000/id/, but they files are size 0 after the move into ~/galaxy-dist/database/files/000 Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Downloading a zip file .......
Hi I can modify the upload.py file by commenting out the uncompress stuff and hence upload a zip file containing many files. However, when I click on the save icon and try and download the file, it seems the tar file is corrupt. I can only assume that during the upload the contents of the files in the zip are somehow being modified? Is this correct? Do you know of any other files I need to modify to be able to download a zip file and not be corrupt? Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Installing galaxy with Apache ...
Hi Jelle, I'm still having issues with Apache. I've moved RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] from /var/www/.htaccess to /etc/apache2/httpd.conf I still get a 404 Not found error when trying to access galaxy (http://140.253.78.44/galaxy ) http://140.253.78.44 still gets the It Works! Apache default index.html and http://140.253.78.44:8080 gets the galaxy page /var/log/apache2/error.log states... [Fri Aug 24 07:35:27 2012] [error] [client 140.253.78.44] File does not exist: /var/www/favicon.ico [Fri Aug 24 07:36:25 2012] [error] [client 140.253.78.44] File does not exist: /var/www/galaxy Now if I change httpd.conf and add the vitrtualHost tags to: ServerName localhost VirtualHost *:80 RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] /VirtualHost I now get a 403 Forbidden error when trying to access (http://140.253.78.44/galaxy ) You don't have permission to access /galaxy/ on this server, and /var/log/apache2/error.log states.. [Fri Aug 24 07:45:33 2012] [error] [client 140.253.78.44] attempt to make remote request from mod_rewrite without proxy enabled: proxy:http://localhost:8080/ [Fri Aug 24 07:45:34 2012] [error] [client 140.253.78.44] File does not exist: /etc/apache2/htdocs Any help much appreciated Neil From: Jelle Scholtalbers [j.scholtalb...@gmail.com] Sent: Thursday, August 23, 2012 8:20 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Installing galaxy with Apache ... Hi Neil, with your current apache configuration, you should probably see Galaxy at http://yourip/galaxy This is due to your Rewriterule /galaxy and for that you have also set proxy_prefix = /galaxy in your universe_wsgi.ini You should probably remove the empty galaxy directory under /var/www Furthermore, most of the time you will not need a directory with 777 in your apache web/documentroot.. Cheers, Jelle On Thu, Aug 23, 2012 at 8:34 AM, neil.burd...@csiro.au wrote: Hi I've installed galaxy with the default settings and it works fine. On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation. After installing Apache I can put my ip address into a browser and I get message saying Apache is working fine. It displays a message from /var/www/index.html Now when I start galaxy I was assuming I would get redirected to the galaxy welcome page, but this doesn't happen and it remains at /var/www/index.html. To view the welcome page I have to add :8080 after the ip address. Is this still required? I thought that Apache would know to redirect to my distributionWhat am I doing wrong? /etc/apache2/sites-available/default-ssl and /etc/apache2/sites-available/default look like this ... DocumentRoot /var/www Directory / Options FollowSymLinks AllowOverride None /Directory Directory /var/www/ Options Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny allow from all /Directory etc ... /var/www/.htaccess RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] I created an empty 'galaxy' directory with 777 permissions on it under /var/www and universe_wsgi.ini # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy #
[galaxy-user] How to upload multiple files......
Hi, I've recently installed galaxy. I was trying to find how to upload multiple files without the need to compress them into a zip/gz file first. Is this possible? As the Get Data option allows only one file at a time. I searched the galaxy archive mailing list but didn't find anything conclusive. I am unable to use ftp client tools due to IT restrictions. Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] file upload renamed
When uploading a file using “Get Data” it seems the file is renamed to
dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to keep
its name rather than being renamed?
It seems this is being done because of the line
${output.dataset.dataset.id}:${output.files_path}:${file_name}
in the upload.xml file. But I don't know where in the code it gets ${file_name}
from. Any ideas how i change this to get the correct name of the file being
uploaded?
Neil
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
