You will need to install from the toolshed ‘Bundle Collection Download a collection of files (Galaxy Version 1.0.1)’- unfortunately this is not currently available on usegalaxy.org.
I have successfully tested this procedure for BAM files (you get a data and an index file) and fastq and fasta files.
1
using the checkbox button in the history panel select all the files you want to export. press the ‘for all selected’ button> and select ‘build dataset list).
Name this list on the next window.
2
The run the tool ‘Bundle Collection’ select the dataset list you just created. This very useful tool, could have better documentation. It is important to understand that it does not create a .zip file but instead creates an .html link whic you can use to download a zip file. If you select the view button of the output dataset of this tool all you will see is a list of datasets which will be in the zip file.
3
The .thml link can be obtained by right clicking the floppy disk icon inside a history item and choosing "Copy Link Location" (for most datasets) or "Download Dataset/Download bam_index"
4
Once you have the <link>, type this (where "$" indicates the terminal prompt), so that the <link> is inside of single quotes. Like many commands, there are many options. These are examples commonly used with Galaxy.
$ wget -O '<link>'
$ wget -O --no-check-certificate '<link>' # ignore SSL certificate warnings
$ wget -c '<link>' # continue an interrupted download
$ curl -o outfile '<link>'
$ curl -o outfile --insecure '<link>' # ignore SSL certificate warnings
$ curl -C - -o outfile '<link>' # continue an interrupted download
I use
curl -o test2.zip 'http://172.XX.X.XXX/galaxy/datasets/f1b20b93d50e5f10/display?to_ext=html'
This generates a zip file called test2
5
you can then
$ unzip test2.zip
this will create a folder called ‘Bundled_Collection’ with all your files (there will be two for each BAM file and one for all others.
Hope this works for you.
Guy
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modified 21 months ago
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21 months ago by
Guy Reeves • 1.0k
