[galaxy-dev] Best practices with data on clusters

2011-12-20 Thread Cittaro Davide
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?

[galaxy-dev] Post...

2011-12-20 Thread Saadeh, Heba
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

[galaxy-dev] Problem uploading file by an URL

2011-12-20 Thread Marc Bras
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

[galaxy-dev] embedded code into Pages

2011-12-20 Thread remy d1
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

Re: [galaxy-dev] problems previewing certain files, downloading files and with login

2011-12-20 Thread Alfonso Núñez Salgado
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

Re: [galaxy-dev] embedded code into Pages

2011-12-20 Thread Jeremy Goecks
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:

[galaxy-dev] Search the Galaxy!

2011-12-20 Thread Dave Clements
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

[galaxy-dev] Problem uploading files from filesystem paths

2011-12-20 Thread Liisa Koski
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

[galaxy-dev] unpacking zip files during upload

2011-12-20 Thread Langhorst, Brad
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