manage data libraries -menu upload files from filesystem paths not present
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/UploadingFile... --> 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/Genom...) 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/UploadingFile... 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
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/UploadingFile... --> 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/Genom...) 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/UploadingFile... 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
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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 <hrh@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=ERP000546<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<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<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<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
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-- Colin Molter University of Brussels - InSilico Team - http://insilico.ulb.ac.be/
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 Hotz<hrh@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=ERP000546<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<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<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<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
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participants (3)
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colin -
colin molter
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Hans-Rudolf Hotz