Hi, Antonio - yes, that's right - FastQC is not 'bundled' and has to
be obtained from the tool authors - we just provide a wrapper to make
it work inside Galaxy.
The Galaxy distribution includes code for some of the inbuilt tools
like the fastq groomer, but most of the distribution tool wrappers
r
Matthew J. Thomas u.washington.edu> writes:
>
>
>
> Hello,
>
> I am working on a local install of Galaxy and when running a test data set I
get this error when invoking the Fastqc commans:
>
> /home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20
> class FastQC():
> ^
> SyntaxEr
Hi Mathew,
The tool xml has a clunky way of finding the fastqc perl script -
which has to be in the same directory as the jars it requires:
rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file
-n "$out_prefix" -f $input_file.ext -e
${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/f
