From gordon@cshl.edu Thu Dec 16 10:45:16 2010
From: Assaf Gordon <gordon@cshl.edu>
To: galaxy-user@lists.galaxyproject.org
Subject: Re: [galaxy-user] fastx barcode-splitter
Date: Thu, 16 Dec 2010 10:45:02 -0500
Message-ID: <4D0A33FE.6090209@cshl.edu>
In-Reply-To: <AANLkTinM+vcQJyHd_CgJmXd+4f0mW_ZT3=O0P6X+HSS4@mail.gmail.com>
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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=20
> 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 workflo=
w editor, and you can't connect them to down-stream tools.

This tool can only be used manually (that is - run it, download the individua=
l files, then run workflows on them).

> I have just started using the fastx barcode splitter tool and found=20
> that the job successfully completed with a tabular list of links to=20
> display results files contents.

Just to clarify: are you getting a tabular (textual file), or an HTML file wi=
th <TABLE> ?
The perl script produces textual output, but the XML galaxy tool should produ=
ce HTML.

> When I  run a 'get data - upload file from your computer' to load=20
> these split files into the galaxy system (as they do not seem to=20
> appear in the history list nor are they automatically accessible to=20
> Galaxy for some strange reason).

Not "a strange reason" - this is by design. That's the way tools with multipl=
e/variable output files work in galaxy (unless there are recent changes to th=
e framework, in which case the tool is slightly out of date)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 :
>=20
> http://localhost:8080/datasets/2d9035b3fc152403/display/Clip_on_data_12__42=
9.txt
> An error occurred running this job: /The uploaded file contains inappropria=
te HTML content

If you look at the error message, it says you've actually managed to upload t=
he 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.txt

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=20
> working methods for reloading the barcode split files?
>=20
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 hre=
f>" 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

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