Possible To Browse Local Filesystem

Question: Possible To Browse Local Filesystem

7.2 years ago by

Dear all, We are setting up a galaxy istance on our server (HPC Cluster with torque and PBS) for internal use. Our problem is that we manage only NGS data (SOLiD and Illumina Data) that are already stored on the server. When we connect to galaxy with our clients we are not able to browse the server file system. Having the possibility to browse the server filesystem would be the best solution for us!! We have look for this funtion but it seems it is not possible... Now, we tried to set up the user directory but adding new file and re-uploading the dir we found duplicated files (it seems that galaxy re-upload every time all the files ignoring if some are already present. This method is OK for us but how can we avoid the file duplications ? In a presentation found on web (blankenberg_pittsburg_2001), we saw that there is the possibility to automatically upload the sequenced reads on Galaxy (and let them available to all our user). Where can we find information for doing this ? All the best Alessandro -- ****************************** Alessandro Albiero Bioinformatics Lab CRIBI-Padua University Viale G. Colombo, 3 35121 Padova-Italy http://genomics.cribi.unipd.it http://genomics.cribi.unipd.it/index.php/User:Albiero Phone. +39. 049 827-6165 Fax. +39. 049 827-6159 ********************************

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modified 7.2 years ago by graham etherington (TSL) • 100 • written 7.2 years ago by alessandro albiero • 10

7.2 years ago by

graham etherington (TSL) • 100

graham etherington (TSL) • 100 wrote:

Alessandro, I'm not sure if I've understood your problem fully, but would creating a directory of sym-links to your data and then pointing the Galaxy Data Libraries to that directory solve your problem? Regards, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 Date: Thu, 6 Oct 2011 17:10:22 +0100 To: "graham etherington (TSL)" <graham.etherington@sainsbury- laboratory.ac.uk<mailto:graham.etherington@sainsbury-="" laboratory.ac.uk="">> Subject: Possible to browse local filesystem Dear all, We are setting up a galaxy istance on our server (HPC Cluster with torque and PBS) for internal use. Our problem is that we manage only NGS data (SOLiD and Illumina Data) that are already stored on the server. When we connect to galaxy with our clients we are not able to browse the server file system. Having the possibility to browse the server filesystem would be the best solution for us!! We have look for this funtion but it seems it is not possible... Now, we tried to set up the user directory but adding new file and re- uploading the dir we found duplicated files (it seems that galaxy re- upload every time all the files ignoring if some are already present. This method is OK for us but how can we avoid the file duplications ? In a presentation found on web (blankenberg_pittsburg_2001), we saw that there is the possibility to automatically upload the sequenced reads on Galaxy (and let them available to all our user). Where can we find information for doing this ? All the best Alessandro -- ****************************** Alessandro Albiero Bioinformatics Lab CRIBI-Padua University Viale G. Colombo, 3 35121 Padova-Italy http://genomics.cribi.unipd.it<http: genomics.cribi.unipd.it=""/> http://genomics.cribi.unipd.it/index.php/User:Albiero Phone. +39. 049 827-6165 Fax. +39. 049 827-6159 ******************************** ___________________________________________________________ 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/ ________________________________ If you reply to this email, your message will be added to the discussion below: http://gmod.827538.n3.nabble.com/Possible-to-browse-local-filesystem- tp3400188p3400188.html To unsubscribe from Galaxy Users, click here<http: gmod.827538.n3.nab="" ble.com="" template="" namlservlet.jtp?macro="unsubscribe_by_code&node=815892" &code="Z3JhaGFtLmV0aGVyaW5ndG9uQHNhaW5zYnVyeS1sYWJvcmF0b3J5LmFjLnVrfDgx" ntg5mnwtmtkwodm3nq="=">.

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