[galaxy-dev] Best practices with data on clusters
Hi developers, I have a question that may be an OT, but since galaxy can work in a clustered environment withh queueing system, I'll try to ask here. Is there anibody here who copies data in a local temporary directory before performing any analysis step and copy it back into the final results? Thanks d Sent from my iPad ___ 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/
[galaxy-dev] Post...
Hello, I would like to be added, in order to be able to post some comments... Regards, heba --- Heba Saadeh Ph.D. Student Dept. of Medical and Molecular Genetics, Medicine School, King's College London, Guy's Hospital, 8th floor Tower Wing, London, SE1 9RT. Office: +44(0)20 7188 3715 ___ 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/
[galaxy-dev] Problem uploading file by an URL
Hi, We have a Galaxy server in production and I have a problem when I want to download a huge file with HTTP URL. Galaxy starts well to download my file, but Galaxy writes this file in / tmp directory. Is it possible to change this directory ? Thank you, Regards, Marc Bras -- Marc Bras -- marc.b...@versailles.inra.fr INRA-URGI: Unité de Recherche Génomique Info Centre de Recherche de Versailles-Grignon Route de Saint Cyr 78026 Versailles - FRANCE Tel: +33 1 30 83 34 70 -- ___ 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/
[galaxy-dev] embedded code into Pages
Hi, I would like to modify Pages a lot. For example, I would like to create a galaxy Page with rss-reader written in PHP (or javascript) in it. I found where content is stored for Pages, but not the script who read this content. Is there any possibility to integrate code into Galaxy Page which could be executed ? Thanks, Regards. ___ 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
Hi, I have found an old thread where Matthew Conte talks about problems previewing certain files, downloading them. Matthew Conte wrote: I'm having several problems with my local galaxy install which may or may not be related to one another.,,The first problem I'm having is with the Display data in browser feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the Display data in browser eyeball icon. It is simply a blank middle panel. I'm having several problems with my local galaxy install which may or may not be related to one another.,,The first problem I'm having is with the Display data in browser feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the Display data in browser eyeball icon. It is simply a blank middle panel. http://gmod.827538.n3.nabble.com/problems-previewing-certain-files-downloading-files-and-with-login-td2919895.html#a3087703 In my case all this happen without a proxy, (so) and I can login in correctly but I still having problem previewing and downloading files. hg summary parent: 6298:b258de1e6cea tip branch: default ___ 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/
Re: [galaxy-dev] embedded code into Pages
I would like to modify Pages a lot. For example, I would like to create a galaxy Page with rss-reader written in PHP (or javascript) in it. I found where content is stored for Pages, but not the script who read this content. Pages uses the WYMEditor to render Pages: http://www.wymeditor.org/ See the wym*.[css/mako/html] and jquery.wymeditor.js files for details. Is there any possibility to integrate code into Galaxy Page which could be executed ? It's not clear exactly what you're looking to do, but Pages includes JS code to load histories/datasets/workflows on expansion. You might look there as a starting point for executing code in Pages. Let us know if you have more questions. Good luck, J. ___ 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/
[galaxy-dev] Search the Galaxy!
Hello all, I am happy to announce that Galaxy now has several Google Custom Searches that make it much easier (really - way, way easier) to find answers to your questions about Galaxy. They are available at http://galaxyproject.org/search/. *Name URL * * Description * ** *Galaxy Web Search http://galaxyproject.org/search/web* http://galaxyproject.org/search/web Searches *everything:* Galaxy Main http://wiki.g2.bx.psu.edu/Main, the mailing list archives http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching, the Galaxy wiki http://wiki.g2.bx.psu.edu/FrontPage, Galaxy's source code at Bitbucket https://bitbucket.org/galaxy/galaxy-central/src/tip/, and the Tool Shed http://wiki.g2.bx.psu.edu/Tool%20Shed. The results are returned in a unified list, and are also grouped into several categories. *Galaxy Mailing List Search http://galaxyproject.org/search/mailinglists* http://galaxyproject.org/search/mailinglists Searches all the Galaxy mailing list archiveshttp://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching. The results are returned in a unified list, and are also grouped by mailing list.** *UseGalaxy Search http://galaxyproject.org/search/usegalaxy* http://galaxyproject.org/search/usegalaxy Search for information about *using* Galaxy. Searches Galaxy Mainhttp://wiki.g2.bx.psu.edu/Main( UseGalaxy.org http://usegalaxy.org/), the wikihttp://wiki.g2.bx.psu.edu/Learn(excluding the Admin http://wiki.g2.bx.psu.edu/Admin pages), and the Galaxy-User and Galaxy-Announce mailing list archiveshttp://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching. *GetGalaxy Search http://galaxyproject.org/search/getgalaxy* http://galaxyproject.org/search/getgalaxy Search for information about installing, customizing, and developing Galaxy. Searches the Galaxy Bitbucket (source) sitehttps://bitbucket.org/galaxy/galaxy-central/src/tip/, the Tool Shed http://toolshed.g2.bx.psu.edu/, the wikihttp://wiki.g2.bx.psu.edu/Admin(excluding the Learn http://wiki.g2.bx.psu.edu/Learn pages), and the Galaxy-Dev and Galaxy-Announce mailing list archiveshttp://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching. We strongly encourage you to give these try. Please send feedback and suggestions to Galaxy Outreach outre...@galaxyproject.org. Happy searching (and a Happy New Year!), Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
[galaxy-dev] Problem uploading files from filesystem paths
Hi, I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error. Any ideas? Thanks in advance, Liisa Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, json_file, output_path ) File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 300, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /usr/lib64/python2.6/subprocess.py, line 633, in __init__ errread, errwrite) File /usr/lib64/python2.6/subprocess.py, line 1139, in _execute_child raise child_exception OSError: [Errno 13] Permission denied ___ 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/
[galaxy-dev] unpacking zip files during upload
I'm working on unpacking a zip file into multiple datasets. I think this is the code path Upload.py UploadToolAction upload_common.py: get_uploaded_datesets new_upload new_history_upload or new_library_upload Then a job gets spooled Which calles add_file in data_source/upload.py And does the expansion of the zip I can unpack the zip and create files in the dataset's path there. But I don't know how to create more dataset associations, and I'm not sure that it makes sense to create datasets on the fly in data_source/upload.py . Should I pass some information along with data_source/upload.py about how to create dataset object and associate them with library/history associations? Or maybe I can pass in some kind of a callback that can handle the dataset expansion? (I'm pretty new to python, but it seems similar to ruby) I thought about a composite dataset, but that seems like overloading that concept. Really the files I'm thinking about uplaoding are 8 independent BAMs or fastqs or whatever – not a set of files that are related to each other. Any suggestions? Brad -- Brad Langhorst New England Biolabs langho...@neb.com ___ 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/
