Re: [galaxy-dev] manage data libraries -menu upload files from filesystem paths not present
Hi Colin In your 'universe_wsgi.ini' file, have you changed the line: library_import_dir = None to the directory with your data? Regards, Hans On 06/28/2011 11:38 AM, colin wrote: Hi, i all, my first post in the mailing list. I started one moth ago galaxy (at the conference) and the tool is really impressive. thx for it. I installed a local version of galaxy (http://ampere.ulb.ac.be), but i am having some trouble when uploading private data on it. Here is the procedure i followed: 1/ I got sra samples from ncbi: http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546 2/ i transformed these sra in fastq format using the sratoolkit https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles -- this provides me fastq files of 25Gb 3/ PROBLEMS: a/ IF I try to upload the data set using an URL in upload file (I created a controller here: http://insilico.ulb.ac.be/publicutilities/sendonthefly?url=/fs1-ampere/GenomicsData/ERP000546/ERR030856.fastq) then only 155Mb are uploaded to galaxy (and no error) b/ if i try to follow that method: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles and i try to get data from the server, the menu upload files from filesystem paths and upload directory of files are not present. == no way to access these files locally any hints for that? thx Colin ___ 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/ ___ 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] manage data libraries -menu upload files from filesystem paths not present
hi, no, i found that just later and that solved the problem. i wanted to cancel my question .. but too late. anyway i managed to put my 35Gb fastq files on galaxy and i am transforming it whith the fastq groomer. any idea about the other problem (upload using url)? which stopped at 155Mb with no error? thx again colin 2011/6/28 Hans-Rudolf Hotz h...@fmi.ch Hi Colin In your 'universe_wsgi.ini' file, have you changed the line: library_import_dir = None to the directory with your data? Regards, Hans On 06/28/2011 11:38 AM, colin wrote: Hi, i all, my first post in the mailing list. I started one moth ago galaxy (at the conference) and the tool is really impressive. thx for it. I installed a local version of galaxy (http://ampere.ulb.ac.be), but i am having some trouble when uploading private data on it. Here is the procedure i followed: 1/ I got sra samples from ncbi: http://trace.ncbi.nlm.nih.gov/**Traces/sra/?study=ERP000546http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546 2/ i transformed these sra in fastq format using the sratoolkit https://bitbucket.org/galaxy/**galaxy-central/wiki/** DataLibraries/UploadingFileshttps://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles -- this provides me fastq files of 25Gb 3/ PROBLEMS: a/ IF I try to upload the data set using an URL in upload file (I created a controller here: http://insilico.ulb.ac.be/** publicutilities/sendonthefly?**url=/fs1-ampere/GenomicsData/** ERP000546/ERR030856.fastqhttp://insilico.ulb.ac.be/publicutilities/sendonthefly?url=/fs1-ampere/GenomicsData/ERP000546/ERR030856.fastq ) then only 155Mb are uploaded to galaxy (and no error) b/ if i try to follow that method: https://bitbucket.org/galaxy/** galaxy-central/wiki/**DataLibraries/UploadingFileshttps://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles and i try to get data from the server, the menu upload files from filesystem paths and upload directory of files are not present. == no way to access these files locally any hints for that? thx Colin __**_ 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/ -- Colin Molter University of Brussels - InSilico Team - http://insilico.ulb.ac.be/ ___ 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] manage data libraries -menu upload files from filesystem paths not present
On 06/28/2011 01:50 PM, colin molter wrote: hi, no, i found that just later and that solved the problem. i wanted to cancel my question .. but too late. anyway i managed to put my 35Gb fastq files on galaxy and i am transforming it whith the fastq groomer. any idea about the other problem (upload using url)? which stopped at 155Mb with no error? No, I just guess it is a browser issue, hence for big files, upload via ftp is recommended, see: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP Hans thx again colin 2011/6/28 Hans-Rudolf Hotzh...@fmi.ch Hi Colin In your 'universe_wsgi.ini' file, have you changed the line: library_import_dir = None to the directory with your data? Regards, Hans On 06/28/2011 11:38 AM, colin wrote: Hi, i all, my first post in the mailing list. I started one moth ago galaxy (at the conference) and the tool is really impressive. thx for it. I installed a local version of galaxy (http://ampere.ulb.ac.be), but i am having some trouble when uploading private data on it. Here is the procedure i followed: 1/ I got sra samples from ncbi: http://trace.ncbi.nlm.nih.gov/**Traces/sra/?study=ERP000546http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546 2/ i transformed these sra in fastq format using the sratoolkit https://bitbucket.org/galaxy/**galaxy-central/wiki/** DataLibraries/UploadingFileshttps://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles -- this provides me fastq files of 25Gb 3/ PROBLEMS: a/ IF I try to upload the data set using an URL in upload file (I created a controller here: http://insilico.ulb.ac.be/** publicutilities/sendonthefly?**url=/fs1-ampere/GenomicsData/** ERP000546/ERR030856.fastqhttp://insilico.ulb.ac.be/publicutilities/sendonthefly?url=/fs1-ampere/GenomicsData/ERP000546/ERR030856.fastq ) then only 155Mb are uploaded to galaxy (and no error) b/ if i try to follow that method: https://bitbucket.org/galaxy/** galaxy-central/wiki/**DataLibraries/UploadingFileshttps://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles and i try to get data from the server, the menu upload files from filesystem paths and upload directory of files are not present. == no way to access these files locally any hints for that? thx Colin __**_ 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/ ___ 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/
