Hi I have been looking into galaxy with a view to finding a platform target for developing code. It is a very ambitious project, and you deserve congratulations for all the development work that has gone into it so far. I have just started using the fastx barcode splitter tool and found that the job successfully completed with a tabular list of links to display results files contents. When I run a 'get data - upload file from your computer' to load these split files into the galaxy system (as they do not seem to appear in the history list nor are they automatically accessible to Galaxy for some strange reason), I can only do this using the URL input field (of get data - upload file from your computer'), then the task fails and get error : http://localhost:8080/datasets/2d9035b3fc152403/display/Clip_on_data_12__429... An error occurred running this job: *The uploaded file contains inappropriate HTML content The fastx documentation say the split files should be written to /tmp , but that it not accessible on the public server the files are not there on my installation. * * Could anyone suggest alternative working methods for reloading the barcode split files? thanks Dr Jan Szubert *
Having sent this note about three weeks ago and had no response, maybe the question I should have asked would be this : Has anyone ever successfully used fastx barcode-splitter.pl inside galaxy ? If so how did you then get the resulting split files back into the galaxy workflow stream? alternatively how do I ask the galaxy admins the same question? Thanks Jan Szubert ---------- Forwarded message ---------- From: Marek Szubert <marek.szubert@gmail.com> Date: 8 December 2010 10:49 Subject: fastx barcode-splitter To: galaxy-user@lists.bx.psu.edu Hi I have been looking into galaxy with a view to finding a platform target for developing code. It is a very ambitious project, and you deserve congratulations for all the development work that has gone into it so far. I have just started using the fastx barcode splitter tool and found that the job successfully completed with a tabular list of links to display results files contents. When I run a 'get data - upload file from your computer' to load these split files into the galaxy system (as they do not seem to appear in the history list nor are they automatically accessible to Galaxy for some strange reason), I can only do this using the URL input field (of get data - upload file from your computer'), then the task fails and get error : http://localhost:8080/datasets/2d9035b3fc152403/display/Clip_on_data_12__429... An error occurred running this job: *The uploaded file contains inappropriate HTML content The fastx documentation say the split files should be written to /tmp , but that it not accessible on the public server the files are not there on my installation. * * Could anyone suggest alternative working methods for reloading the barcode split files? thanks Dr Jan Szubert *
Hello Jan, Marek Szubert wrote, On 12/16/2010 09:24 AM:
If so how did you then get the resulting split files back into the galaxy workflow stream?
If you mean the graphical workflow editor, then the simple answer is "you can't" (to the best of my knowledge). This tool produces a variable number of output files, using the "output.files_path" feature of galaxy. Those output files will not be shown in the workflow editor, and you can't connect them to down-stream tools. This tool can only be used manually (that is - run it, download the individual files, then run workflows on them).
I have just started using the fastx barcode splitter tool and found that the job successfully completed with a tabular list of links to display results files contents.
Just to clarify: are you getting a tabular (textual file), or an HTML file with <TABLE> ? The perl script produces textual output, but the XML galaxy tool should produce HTML.
When I run a 'get data - upload file from your computer' to load these split files into the galaxy system (as they do not seem to appear in the history list nor are they automatically accessible to Galaxy for some strange reason).
Not "a strange reason" - this is by design. That's the way tools with multiple/variable output files work in galaxy (unless there are recent changes to the framework, in which case the tool is slightly out of date)
I can only do this using the URL input field (of get data - upload file from your computer'), then the task fails and get error :
http://localhost:8080/datasets/2d9035b3fc152403/display/Clip_on_data_12__429... An error occurred running this job: /The uploaded file contains inappropriate HTML content
If you look at the error message, it says you've actually managed to upload the file, but for some reason it contains HTML file. Can you try to download the file from the command line? run: wget http://localhost:8080/datasets/2d9035b3fc152403/display/Clip_on_data_12__429... And see if you get the FASTQ output, or something else.
The fastx documentation say the split files should be written to /tmp , but that it not accessible on the public server the files are not there on my installation. / / Could anyone suggest alternative working methods for reloading the barcode split files?
On your local galaxy instance, you can change the tool to write to files in a directory that is accessible from a public server. This is the way the tool worked before galaxy supported variable output files. 1. In "fastx_barcode_splitter.xml", change the "$output.files_path" (line 3) to a hard-coded directory path that is accessible from your web server. 2. In "fastx_barcode_splitter_galaxy_wrapper.sh", line 79, change the "<a href>" to include the URL that corresponds to the directory above. This will produce HTML files in which the links to the files are pointing to the right place. Regards, -gordon
participants (2)
-
Assaf Gordon -
Marek Szubert